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Ahmed NI, Khandelwal N, Anderson AG, Oh E, Vollmer RM, Kulkarni A, Gibson JR, Konopka G. Compensation between FOXP transcription factors maintains proper striatal function. Cell Rep 2024; 43:114257. [PMID: 38761373 DOI: 10.1016/j.celrep.2024.114257] [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: 07/25/2023] [Revised: 02/05/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024] Open
Abstract
Spiny projection neurons (SPNs) of the striatum are critical in integrating neurochemical information to coordinate motor and reward-based behavior. Mutations in the regulatory transcription factors expressed in SPNs can result in neurodevelopmental disorders (NDDs). Paralogous transcription factors Foxp1 and Foxp2, which are both expressed in the dopamine receptor 1 (D1) expressing SPNs, are known to have variants implicated in NDDs. Utilizing mice with a D1-SPN-specific loss of Foxp1, Foxp2, or both and a combination of behavior, electrophysiology, and cell-type-specific genomic analysis, loss of both genes results in impaired motor and social behavior as well as increased firing of the D1-SPNs. Differential gene expression analysis implicates genes involved in autism risk, electrophysiological properties, and neuronal development and function. Viral-mediated re-expression of Foxp1 into the double knockouts is sufficient to restore electrophysiological and behavioral deficits. These data indicate complementary roles between Foxp1 and Foxp2 in the D1-SPNs.
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Affiliation(s)
- Newaz I Ahmed
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Nitin Khandelwal
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Ashley G Anderson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Emily Oh
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Rachael M Vollmer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Jay R Gibson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA.
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Ding C, Zhou W, Shi Y, Shan S, Yuan Y, Zhang Y, Li F, Qiu Z. Srcap haploinsufficiency induced autistic-like behaviors in mice through disruption of Satb2 expression. Cell Rep 2024; 43:114231. [PMID: 38733588 DOI: 10.1016/j.celrep.2024.114231] [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: 02/03/2024] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Mutations in the SRCAP gene are among the genetic alterations identified in autism spectrum disorders (ASD). However, the pathogenic mechanisms remain unclear. In this study, we demonstrate that Srcap+/- mice manifest deficits in social novelty response, as well as increased repetitive behaviors, anxiety, and impairments in learning and memory. Notably, a reduction in parvalbumin-positive neurons is observed in the retrosplenial cortex (RSC) and dentate gyrus (DG) of these mice. Through RNA sequencing, we identify dysregulation in 27 ASD-related genes in Srcap+/- mice. Specifically, we find that Srcap regulates expression of Satb2 via H2A.z in the promoter. Therapeutic intervention via retro-orbital injection of adeno-associated virus (AAV)-Satb2 in neonatal Srcap+/- mice leads to amelioration of the neurodevelopmental and ASD-like abnormalities. Furthermore, the expression of Satb2 only in the RSC of adolescent mice rectifies social novelty impairments. These results underscore the pivotal role of Srcap in neurodevelopment, by regulating Satb2, providing valuable insights for the pathophysiology of ASD.
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Affiliation(s)
- Chaodong Ding
- Songjiang Research Institute, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Zhou
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Developmental and Behavioral Pediatric & Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhan Shi
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Shifang Shan
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yiting Yuan
- Songjiang Research Institute, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuefang Zhang
- Songjiang Research Institute, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Li
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Developmental and Behavioral Pediatric & Child Primary Care, Brain and Behavioral Research Unit of Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zilong Qiu
- Songjiang Research Institute, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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3
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Courchesne E, Taluja V, Nazari S, Aamodt CM, Pierce K, Duan K, Stophaeros S, Lopez L, Barnes CC, Troxel J, Campbell K, Wang T, Hoekzema K, Eichler EE, Nani JV, Pontes W, Sanchez SS, Lombardo MV, de Souza JS, Hayashi MAF, Muotri AR. Embryonic origin of two ASD subtypes of social symptom severity: the larger the brain cortical organoid size, the more severe the social symptoms. Mol Autism 2024; 15:22. [PMID: 38790065 PMCID: PMC11127428 DOI: 10.1186/s13229-024-00602-8] [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: 12/05/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Social affective and communication symptoms are central to autism spectrum disorder (ASD), yet their severity differs across toddlers: Some toddlers with ASD display improving abilities across early ages and develop good social and language skills, while others with "profound" autism have persistently low social, language and cognitive skills and require lifelong care. The biological origins of these opposite ASD social severity subtypes and developmental trajectories are not known. METHODS Because ASD involves early brain overgrowth and excess neurons, we measured size and growth in 4910 embryonic-stage brain cortical organoids (BCOs) from a total of 10 toddlers with ASD and 6 controls (averaging 196 individual BCOs measured/subject). In a 2021 batch, we measured BCOs from 10 ASD and 5 controls. In a 2022 batch, we tested replicability of BCO size and growth effects by generating and measuring an independent batch of BCOs from 6 ASD and 4 control subjects. BCO size was analyzed within the context of our large, one-of-a-kind social symptom, social attention, social brain and social and language psychometric normative datasets ranging from N = 266 to N = 1902 toddlers. BCO growth rates were examined by measuring size changes between 1- and 2-months of organoid development. Neurogenesis markers at 2-months were examined at the cellular level. At the molecular level, we measured activity and expression of Ndel1; Ndel1 is a prime target for cell cycle-activated kinases; known to regulate cell cycle, proliferation, neurogenesis, and growth; and known to be involved in neuropsychiatric conditions. RESULTS At the BCO level, analyses showed BCO size was significantly enlarged by 39% and 41% in ASD in the 2021 and 2022 batches. The larger the embryonic BCO size, the more severe the ASD social symptoms. Correlations between BCO size and social symptoms were r = 0.719 in the 2021 batch and r = 0. 873 in the replication 2022 batch. ASD BCOs grew at an accelerated rate nearly 3 times faster than controls. At the cell level, the two largest ASD BCOs had accelerated neurogenesis. At the molecular level, Ndel1 activity was highly correlated with the growth rate and size of BCOs. Two BCO subtypes were found in ASD toddlers: Those in one subtype had very enlarged BCO size with accelerated rate of growth and neurogenesis; a profound autism clinical phenotype displaying severe social symptoms, reduced social attention, reduced cognitive, very low language and social IQ; and substantially altered growth in specific cortical social, language and sensory regions. Those in a second subtype had milder BCO enlargement and milder social, attention, cognitive, language and cortical differences. LIMITATIONS Larger samples of ASD toddler-derived BCO and clinical phenotypes may reveal additional ASD embryonic subtypes. CONCLUSIONS By embryogenesis, the biological bases of two subtypes of ASD social and brain development-profound autism and mild autism-are already present and measurable and involve dysregulated cell proliferation and accelerated neurogenesis and growth. The larger the embryonic BCO size in ASD, the more severe the toddler's social symptoms and the more reduced the social attention, language ability, and IQ, and the more atypical the growth of social and language brain regions.
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Affiliation(s)
- Eric Courchesne
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA.
| | - Vani Taluja
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Sanaz Nazari
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Caitlin M Aamodt
- Department of Pediatrics and Department of Molecular and Cellular Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Kuaikuai Duan
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Sunny Stophaeros
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Cynthia Carter Barnes
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Jaden Troxel
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Kathleen Campbell
- Autism Center of Excellence, Department of Neurosciences, University of California, San Diego, 8110 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
- Neuroscience Research Institute, Peking University, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of China, Beijing, 100191, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Joao V Nani
- Department of Pediatrics and Department of Molecular and Cellular Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Wirla Pontes
- Department of Pediatrics and Department of Molecular and Cellular Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
| | - Sandra Sanchez Sanchez
- Department of Pediatrics and Department of Molecular and Cellular Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
| | - Michael V Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Janaina S de Souza
- Department of Pediatrics and Department of Molecular and Cellular Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
| | - Mirian A F Hayashi
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Alysson R Muotri
- Department of Pediatrics and Department of Molecular and Cellular Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA.
- Rady Children's Hospital, Center for Academic Research and Training in Anthropogeny (CARTA), Archealization Center (ArchC), Kavli Institute for Brain and Mind, La Jolla, CA, USA.
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4
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Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen AA, Nowakowski TJ, Ahituv N, Pollard KS. Massively parallel characterization of regulatory elements in the developing human cortex. Science 2024; 384:eadh0559. [PMID: 38781390 DOI: 10.1126/science.adh0559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.
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Affiliation(s)
- Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sean Whalen
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marilyn Steyert
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA 94158, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Ryan Ziffra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Daniela A Pereira
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
- Graduate Program of Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Davide Capauto
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520, USA
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Alex A Pollen
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
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5
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Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 2024; 384:eadh7688. [PMID: 38781356 DOI: 10.1126/science.adh7688] [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: 03/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders; yet, the role of cell type-specific splicing and transcript-isoform diversity during human brain development has not been systematically investigated. In this work, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone and cortical plate regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 distinct isoforms, of which 72.6% were novel (not previously annotated in Gencode version 33), and uncovered a substantial contribution of transcript-isoform diversity-regulated by RNA binding proteins-in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to reprioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders.
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Affiliation(s)
- Ashok Patowary
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Connor Jops
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Celine K Vuong
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xinzhou Ge
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Minsoo Kim
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Naihua Gong
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Vo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jingyi Jessica Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
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6
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Novarino G, Bock C. Mapping the brain's gene-regulatory maze. Science 2024; 384:860-861. [PMID: 38781359 DOI: 10.1126/science.adp4663] [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: 05/25/2024]
Abstract
DNA sequences are connected to genes and functions in the developing and adult brain.
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Affiliation(s)
- Gaia Novarino
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
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7
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Wamsley B, Bicks L, Cheng Y, Kawaguchi R, Quintero D, Margolis M, Grundman J, Liu J, Xiao S, Hawken N, Mazariegos S, Geschwind DH. Molecular cascades and cell type-specific signatures in ASD revealed by single-cell genomics. Science 2024; 384:eadh2602. [PMID: 38781372 DOI: 10.1126/science.adh2602] [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: 02/21/2023] [Accepted: 02/28/2024] [Indexed: 05/25/2024]
Abstract
Genomic profiling in postmortem brain from autistic individuals has consistently revealed convergent molecular changes. What drives these changes and how they relate to genetic susceptibility in this complex condition are not well understood. We performed deep single-nucleus RNA sequencing (snRNA-seq) to examine cell composition and transcriptomics, identifying dysregulation of cell type-specific gene regulatory networks (GRNs) in autism spectrum disorder (ASD), which we corroborated using single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) and spatial transcriptomics. Transcriptomic changes were primarily cell type specific, involving multiple cell types, most prominently interhemispheric and callosal-projecting neurons, interneurons within superficial laminae, and distinct glial reactive states involving oligodendrocytes, microglia, and astrocytes. Autism-associated GRN drivers and their targets were enriched in rare and common genetic risk variants, connecting autism genetic susceptibility and cellular and circuit alterations in the human brain.
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Affiliation(s)
- Brie Wamsley
- Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer Grundman
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Natalie Hawken
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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8
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Aguzzoli Heberle B, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nat Biotechnol 2024:10.1038/s41587-024-02245-9. [PMID: 38778214 DOI: 10.1038/s41587-024-02245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Determining whether the RNA isoforms from medically relevant genes have distinct functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a step toward this goal for neurological diseases, we sequenced 12 postmortem, aged human frontal cortices (6 Alzheimer disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. We identified 1,917 medically relevant genes expressing multiple isoforms in the frontal cortex where 1,018 had multiple isoforms with different protein-coding sequences. Of these 1,018 genes, 57 are implicated in brain-related diseases including major depression, schizophrenia, Parkinson's disease and Alzheimer disease. Our study also uncovered 53 new RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. We also reported on five mitochondrially encoded, spliced RNA isoforms. We found 99 differentially expressed RNA isoforms between cases with Alzheimer disease and controls.
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Affiliation(s)
- Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - J Anthony Brandon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Madeline L Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Kayla A Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Ketsile I Dikobe
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Brendan J White
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Lacey A Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Grant A Fox
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Mark E Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Patricia H Doyle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Brittney A Williams
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Edward J Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mina Ryten
- UK Dementia Research Institute at The University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Justin B Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA.
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA.
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9
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Silva DB, Trinidad M, Ljungdahl A, Revalde JL, Berguig GY, Wallace W, Patrick CS, Bomba L, Arkin M, Dong S, Estrada K, Hutchinson K, LeBowitz JH, Schlessinger A, Johannesen KM, Møller RS, Giacomini KM, Froelich S, Sanders SJ, Wuster A. Haploinsufficiency underlies the neurodevelopmental consequences of SLC6A1 variants. Am J Hum Genet 2024:S0002-9297(24)00162-9. [PMID: 38781976 DOI: 10.1016/j.ajhg.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Heterozygous variants in SLC6A1, encoding the GAT-1 GABA transporter, are associated with seizures, developmental delay, and autism. The majority of affected individuals carry missense variants, many of which are recurrent germline de novo mutations, raising the possibility of gain-of-function or dominant-negative effects. To understand the functional consequences, we performed an in vitro GABA uptake assay for 213 unique variants, including 24 control variants. De novo variants consistently resulted in a decrease in GABA uptake, in keeping with haploinsufficiency underlying all neurodevelopmental phenotypes. Where present, ClinVar pathogenicity reports correlated well with GABA uptake data; the functional data can inform future reports for the remaining 72% of unscored variants. Surface localization was assessed for 86 variants; two-thirds of loss-of-function missense variants prevented GAT-1 from being present on the membrane while GAT-1 was on the surface but with reduced activity for the remaining third. Surprisingly, recurrent de novo missense variants showed moderate loss-of-function effects that reduced GABA uptake with no evidence for dominant-negative or gain-of-function effects. Using linear regression across multiple missense severity scores to extrapolate the functional data to all potential SLC6A1 missense variants, we observe an abundance of GAT-1 residues that are sensitive to substitution. The extent of this missense vulnerability accounts for the clinically observed missense enrichment; overlap with hypermutable CpG sites accounts for the recurrent missense variants. Strategies to increase the expression of the wild-type SLC6A1 allele are likely to be beneficial across neurodevelopmental disorders, though the developmental stage and extent of required rescue remain unknown.
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Affiliation(s)
- Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Marena Trinidad
- BioMarin Pharmaceutical Inc., Novato, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK
| | - Jezrael L Revalde
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Cory S Patrick
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Michelle Arkin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katrine M Johannesen
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Rikke S Møller
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Member of ERN Epicare, Danish Epilepsy Centre, Dianalund, Denmark
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK.
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10
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Wu R, Li X, Meng Z, Li P, He Z, Liang L. Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing. Orphanet J Rare Dis 2024; 19:205. [PMID: 38764027 PMCID: PMC11103872 DOI: 10.1186/s13023-024-03214-w] [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: 02/20/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Trio-based whole-exome sequencing (trio-WES) enables identification of pathogenic variants, including copy-number variants (CNVs), in children with unexplained neurodevelopmental delay (NDD) and neurodevelopmental comorbidities (NDCs), including autism spectrum disorder (ASD), epilepsy, and attention deficit hyperactivity disorder. Further phenotypic and genetic analysis on trio-WES-tested NDD-NDCs cases may help to identify key phenotypic factors related to higher diagnostic yield of using trio-WES and novel risk genes associated with NDCs in clinical settings. METHODS In this study, we retrospectively performed phenotypic analysis on 163 trio-WES-tested NDD-NDCs children to determine the phenotypic differences between genetically diagnosed and non-genetically diagnosed groups. Additionally, we conducted genetic analysis of ASD genes with the help of Simons Foundation for Autism Research Institute (SFARI) Gene database to identify novel possible ASD-risk genes underlying genetic NDD conditions. RESULTS Among these 163 patients, pathogenic variants were identified in 82 cases (82/163, 50.3%), including 20 cases with CNVs. By comparing phenotypic variables between genetically diagnosed group (82 cases) and non-genetically diagnosed group (81 cases) with multivariate binary logistic regression analysis, we revealed that NDD-NDCs cases presenting with severe-profound NDD [53/82 vs 17/81, adjusted-OR (95%CI): 4.865 (2.213 - 10.694), adjusted-P < 0.001] or having multiple NDCs [26/82 vs 8/81, adjusted-OR (95%CI): 3.731 (1.399 - 9.950), adjusted-P = 0.009] or accompanying ASD [64/82 vs 35/81, adjusted-OR (95%CI): 3.256 (1.479 - 7.168), adjusted-P = 0.003] and head circumference abnormality [33/82 vs 11/81, adjusted-OR (95%CI): 2.788 (1.148 - 6.774), adjusted-P = 0.024] were more likely to have a genetic diagnosis using trio-WES. Moreover, 37 genes with monogenetic variants were identified in 48 patients genetically diagnosed with NDD-ASD, and 15 dosage-sensitive genes were identified in 16 individuals with NDD-ASD carrying CNVs. Most of those genes had been proven to be ASD-related genes. However, some of them (9 genes) were not proven sufficiently to correlate with ASD. By literature review and constructing protein-protein interaction networks among these 9 candidate ASD-risk genes and 102 established ASD genes obtained from the SFARI Gene database, we identified CUL4B, KCNH1, and PLA2G6 as novel possible ASD-risk genes underlying genetic NDD conditions. CONCLUSIONS Trio-WES testing is recommended for patients with unexplained NDD-NDCs that have severe-profound NDD or multiple NDCs, particularly those with accompanying ASD and head circumference abnormality, as these independent factors may increase the likelihood of genetic diagnosis using trio-WES. Moreover, NDD patients with pathogenic variants in CUL4B, KCNH1 and PLA2G6 should be aware of potential risks of developing ASD during their disease courses.
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Affiliation(s)
- Ruohao Wu
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Xiaojuan Li
- Department of Research and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Zhe Meng
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Pinggan Li
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Zhanwen He
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
| | - Liyang Liang
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
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11
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Cai W, Song W, Yu S, Zhao M, Lin GN. Human lineage mutations regulate RNA-protein binding of conserved genes NTRK2 and ITPR1 involved in human evolution. Gen Psychiatr 2024; 37:e101425. [PMID: 38770356 PMCID: PMC11103204 DOI: 10.1136/gpsych-2023-101425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/14/2024] [Indexed: 05/22/2024] Open
Abstract
Background The role of human lineage mutations (HLMs) in human evolution through post-transcriptional modification is unclear. Aims To investigate the contribution of HLMs to human evolution through post-transcriptional modification. Methods We applied a deep learning model Seqweaver to predict how HLMs impact RNA-binding protein affinity. Results We found that only 0.27% of HLMs had significant impacts on RNA-binding proteins at the threshold of the top 1% of human common variations. These HLMs enriched in a set of conserved genes highly expressed in adult excitatory neurons and prenatal Purkinje neurons, and were involved in synapse organisation and the GTPase pathway. These genes also carried excess damaging coding mutations that caused neurodevelopmental disorders, ataxia and schizophrenia. Among these genes, NTRK2 and ITPR1 had the most aggregated evidence of functional importance, suggesting their essential roles in cognition and bipedalism. Conclusions Our findings suggest that a small subset of human-specific mutations have contributed to human speciation through impacts on post-transcriptional modification of critical brain-related genes.
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Affiliation(s)
- Wenxiang Cai
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Shunying Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Min Zhao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
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12
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Zhang S, Mi P, Luan J, Sun M, Zhao X, Feng X. Fluorene-9-bisphenol acts on the gut-brain axis by regulating oxytocin signaling to disturb social behaviors in zebrafish. ENVIRONMENTAL RESEARCH 2024; 255:119169. [PMID: 38763277 DOI: 10.1016/j.envres.2024.119169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/21/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Previous studies have identified the exposure to ubiquitous environmental endocrine disruptors may be a risk factor of neurological disorders. However, the effects of fluorene-9-bisphenol (BHPF) in environmental exposure concentrations associated with these disorders are poorly understood. In this study, classic light-dark and social behavior tests were performed on zebrafish larvae and adults exposed BHPF exposure to evaluate social behavioral disorders and the microbiota-gut-brain axis was assessed to reveal the potential mechanisms underlying the behavioral abnormalities observed. Our results demonstrated that zebrafish larvae exposed to an environmentally relevant concentration (0.1 nM) of BHPF for 7 days showed a diminished response to external environmental factors (light or dark). Zebrafish larvae exposed to BHPF for 7 days or adults exposed to BHPF for 30 days at 1 μM displayed significant behavioral inhibition and altered social behaviors, including social recognition, social preference, and social fear contagion, indicating autism-like behaviors were induced by the exposure. BHPF exposure reduced the distribution of Nissl bodies in midbrain neurons and significantly reduced 5-hydroxytryptamine signaling. Oxytocin (OXT) levels and expression of its receptor oxtra in the gut and brain were down-regulated by BHPF exposure. In addition, the expression levels of genes related to the excitation-inhibitory balance of synaptic transmission changed. Microbiomics revealed increased community diversity and altered abundance of some microflora, such as an elevation in Bacillota and Bacteroidota and a decline in Mycoplasmatota in zebrafish guts, which might contribute to the abnormal neural circuits and autism-like behaviors induced by BHPF. Finally, the rescue effect of exogenous OXT on social behavioral defects induced by BHPF exposure was verified in zebrafish, highlighting the crucial role of OXT signaling through gut-brain axis in the regulatory mechanisms of social behaviors affected by BHPF. This study contributes to understanding the effects of environmental BHPF exposure on neuropsychiatric disorders and attracts public attention to the health risks posed by chemicals in aquatic organisms. The potential mental disorders should be considered in the safety assessments of environmental pollutants.
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Affiliation(s)
- Shuhui Zhang
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education. Nankai University, Tianjin, 300071, China
| | - Ping Mi
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Jialu Luan
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education. Nankai University, Tianjin, 300071, China
| | - Mingzhu Sun
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China
| | - Xin Zhao
- The Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, 300071, China.
| | - Xizeng Feng
- College of Life Science, State Key Laboratory of Medicinal Chemical Biology, The Key Laboratory of Bioactive Materials, Ministry of Education. Nankai University, Tianjin, 300071, China.
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13
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Gao Y, Dong Q, Arachchilage KH, Risgaard R, Sheng J, Syed M, Schmidt DK, Jin T, Liu S, Knaack SA, Doherty D, Glass I, Levine JE, Wang D, Chang Q, Zhao X, Sousa AM. Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.02.543460. [PMID: 37398253 PMCID: PMC10312516 DOI: 10.1101/2023.06.02.543460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The prefrontal cortex (PFC) is critical for myriad high-cognitive functions and is associated with several neuropsychiatric disorders. Here, using Patch-seq and single-nucleus multiomic analyses, we identified genes and regulatory networks governing the maturation of distinct neuronal populations in the PFC of rhesus macaque. We discovered that specific electrophysiological properties exhibited distinct maturational kinetics and identified key genes underlying these properties. We unveiled that RAPGEF4 is important for the maturation of resting membrane potential and inward sodium current in both macaque and human. We demonstrated that knockdown of CHD8, a high-confidence autism risk gene, in human and macaque organotypic slices led to impaired maturation, via downregulation of key genes, including RAPGEF4. Restoring the expression of RAPGEF4 rescued the proper electrophysiological maturation of CHD8-deficient neurons. Our study revealed regulators of neuronal maturation during a critical period of PFC development in primates and implicated such regulators in molecular processes underlying autism.
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14
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Kraft J, Braun A, Awasthi S, Panagiotaropoulou G, Schipper M, Bell N, Posthuma D, Pardiñas AF, Ripke S, Heilbron K. Identifying drug targets for schizophrenia through gene prioritization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307423. [PMID: 38798390 PMCID: PMC11118622 DOI: 10.1101/2024.05.15.24307423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Schizophrenia genome-wide association studies (GWASes) have identified >250 significant loci and prioritized >100 disease-related genes. However, gene prioritization efforts have mostly been restricted to locus-based methods that ignore information from the rest of the genome. Methods To more accurately characterize genes involved in schizophrenia etiology, we applied a combination of highly-predictive tools to a published GWAS of 67,390 schizophrenia cases and 94,015 controls. We combined both locus-based methods (fine-mapped coding variants, distance to GWAS signals) and genome-wide methods (PoPS, MAGMA, ultra-rare coding variant burden tests). To validate our findings, we compared them with previous prioritization efforts, known neurodevelopmental genes, and results from the PsyOPS tool. Results We prioritized 62 schizophrenia genes, 41 of which were also highlighted by our validation methods. In addition to DRD2 , the principal target of antipsychotics, we prioritized 9 genes that are targeted by approved or investigational drugs. These included drugs targeting glutamatergic receptors ( GRIN2A and GRM3 ), calcium channels ( CACNA1C and CACNB2 ), and GABA B receptor ( GABBR2 ). These also included genes in loci that are shared with an addiction GWAS ( e.g. PDE4B and VRK2 ). Conclusions We curated a high-quality list of 62 genes that likely play a role in the development of schizophrenia. Developing or repurposing drugs that target these genes may lead to a new generation of schizophrenia therapies. Rodent models of addiction more closely resemble the human disorder than rodent models of schizophrenia. As such, genes prioritized for both disorders could be explored in rodent addiction models, potentially facilitating drug development.
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15
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Andrews DS, Diers K, Lee JK, Harvey DJ, Heath B, Cordero D, Rogers SJ, Reuter M, Solomon M, Amaral DG, Nordahl CW. Sex differences in trajectories of cortical development in autistic children from 2-13 years of age. Mol Psychiatry 2024:10.1038/s41380-024-02592-8. [PMID: 38755243 DOI: 10.1038/s41380-024-02592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024]
Abstract
Previous studies have reported alterations in cortical thickness in autism. However, few have included enough autistic females to determine if there are sex specific differences in cortical structure in autism. This longitudinal study aimed to investigate autistic sex differences in cortical thickness and trajectory of cortical thinning across childhood. Participants included 290 autistic (88 females) and 139 nonautistic (60 females) individuals assessed at up to 4 timepoints spanning ~2-13 years of age (918 total MRI timepoints). Estimates of cortical thickness in early and late childhood as well as the trajectory of cortical thinning were modeled using spatiotemporal linear mixed effects models of age-by-sex-by-diagnosis. Additionally, the spatial correspondence between cortical maps of sex-by-diagnosis differences and neurotypical sex differences were evaluated. Relative to their nonautistic peers, autistic females had more extensive cortical differences than autistic males. These differences involved multiple functional networks, and were mainly characterized by thicker cortex at ~3 years of age and faster cortical thinning in autistic females. Cortical regions in which autistic alterations were different between the sexes significantly overlapped with regions that differed by sex in neurotypical development. Autistic females and males demonstrated some shared differences in cortical thickness and rate of cortical thinning across childhood relative to their nonautistic peers, however these areas were relatively small compared to the widespread differences observed across the sexes. These results support evidence of sex-specific neurobiology in autism and suggest that processes that regulate sex differentiation in the neurotypical brain contribute to sex differences in the etiology of autism.
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Affiliation(s)
- Derek S Andrews
- Department of Psychiatry & Behavioral Sciences, the MIND Institute, University of California, Davis, CA, USA.
| | - Kersten Diers
- AI in Medical Imaging, German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Joshua K Lee
- Department of Psychiatry & Behavioral Sciences, the MIND Institute, University of California, Davis, CA, USA
| | - Danielle J Harvey
- Division of Biostatistics, Department of Public Health Sciences, University of California, University of California, Davis, CA, USA
| | - Brianna Heath
- Department of Psychiatry & Behavioral Sciences, the MIND Institute, University of California, Davis, CA, USA
| | - Devani Cordero
- A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | - Sally J Rogers
- Department of Psychiatry & Behavioral Sciences, the MIND Institute, University of California, Davis, CA, USA
| | - Martin Reuter
- AI in Medical Imaging, German Center for Neurodegenerative Diseases, Bonn, Germany
- A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Marjorie Solomon
- Department of Psychiatry & Behavioral Sciences, the MIND Institute, University of California, Davis, CA, USA
| | - David G Amaral
- Department of Psychiatry & Behavioral Sciences, the MIND Institute, University of California, Davis, CA, USA
| | - Christine Wu Nordahl
- Department of Psychiatry & Behavioral Sciences, the MIND Institute, University of California, Davis, CA, USA
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Gerik-Celebi HB, Bolat H, Unsel-Bolat G. Rare heterozygous genetic variants of NRXN and NLGN gene families involved in synaptic function and their association with neurodevelopmental disorders. Dev Neurobiol 2024. [PMID: 38739110 DOI: 10.1002/dneu.22941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/02/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
The interaction of neurexins (NRXNs) in the presynaptic membrane with postsynaptic cell adhesion molecules called neuroligins (NLGNs) is critical for this synaptic function. Impaired synaptic functions are emphasized in neurodevelopmental disorders to uncover etiological factors. We evaluated variants in NRXN and NLGN genes encoding molecules located directly at the synapse in patients with neuropsychiatric disorders using clinical exome sequencing and chromosomal microarray. We presented detailed clinical findings of cases carrying heterozygous NRXN1 (c.190C > T, c.1679C > T and two copy number variations [CNVs]), NRXN2 (c.808dup, c.1901G > T), NRXN3 (c.3889C > T), and NLGN1 (c.269C > G, c.473T > A) gene variants. In addition, three novel variants were identified in the NRXN1 (c.1679C > T), NRXN3 [c.3889C > T (p.Pro1297Ser)], and NLGN1 [c.473T > A (p.Ile158Lys)] genes. We emphasize the clinical findings of CNVs of the NRXN1 gene causing a more severe clinical presentation than single nucleotide variants of the NRXN1 gene in this study. We detected an NRXN2 gene variant (c.808dup) with low allelic frequency in two unrelated cases with the same diagnosis. We emphasize the importance of this variant for future studies. We suggest that NRXN2, NRXN3, and NLGN1 genes, which are less frequently reported than NRXN1 gene variants, may also be associated with neurodevelopmental disorders.
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Affiliation(s)
| | - Hilmi Bolat
- Department of Medical Genetics, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Gul Unsel-Bolat
- Department of Child and Adolescent Psychiatry, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
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17
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Cording KR, Tu EM, Wang H, Agopyan-Miu AHCW, Bateup HS. Cntnap2 loss drives striatal neuron hyperexcitability and behavioral inflexibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593387. [PMID: 38766169 PMCID: PMC11100810 DOI: 10.1101/2024.05.09.593387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by two major diagnostic criteria - persistent deficits in social communication and interaction, and the presence of restricted, repetitive patterns of behavior (RRBs). Evidence from both human and animal model studies of ASD suggest that alteration of striatal circuits, which mediate motor learning, action selection, and habit formation, may contribute to the manifestation of RRBs. CNTNAP2 is a syndromic ASD risk gene, and loss of function of Cntnap2 in mice is associated with RRBs. How loss of Cntnap2 impacts striatal neuron function is largely unknown. In this study, we utilized Cntnap2-/- mice to test whether altered striatal neuron activity contributes to aberrant motor behaviors relevant to ASD. We find that Cntnap2-/- mice exhibit increased cortical drive of striatal projection neurons (SPNs), with the most pronounced effects in direct pathway SPNs. This enhanced drive is likely due to increased intrinsic excitability of SPNs, which make them more responsive to cortical inputs. We also find that Cntnap2-/- mice exhibit spontaneous repetitive behaviors, increased motor routine learning, and cognitive inflexibility. Increased corticostriatal drive, in particular of the direct pathway, may contribute to the acquisition of repetitive, inflexible behaviors in Cntnap2 mice.
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Affiliation(s)
- Katherine R. Cording
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA USA
| | - Emilie M. Tu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA USA
| | - Hongli Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA USA
| | | | - Helen S. Bateup
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA USA
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18
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Noel JP, Balzani E, Acerbi L, Benson J, Savin C, Angelaki DE. A common computational and neural anomaly across mouse models of autism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593232. [PMID: 38766250 PMCID: PMC11100696 DOI: 10.1101/2024.05.08.593232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Computational psychiatry has suggested that humans within the autism spectrum disorder (ASD) inflexibly update their expectations (i.e., Bayesian priors). Here, we leveraged high-yield rodent psychophysics (n = 75 mice), extensive behavioral modeling (including principled and heuristics), and (near) brain-wide single cell extracellular recordings (over 53k units in 150 brain areas) to ask (1) whether mice with different genetic perturbations associated with ASD show this same computational anomaly, and if so, (2) what neurophysiological features are shared across genotypes in subserving this deficit. We demonstrate that mice harboring mutations in Fmr1 , Cntnap2 , and Shank3B show a blunted update of priors during decision-making. Neurally, the differentiating factor between animals flexibly and inflexibly updating their priors was a shift in the weighting of prior encoding from sensory to frontal cortices. Further, in mouse models of ASD frontal areas showed a preponderance of units coding for deviations from the animals' long-run prior, and sensory responses did not differentiate between expected and unexpected observations. These findings demonstrate that distinct genetic instantiations of ASD may yield common neurophysiological and behavioral phenotypes.
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19
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Zhang Y, Ahsan MU, Wang K. Noncoding de novo mutations in SCN2A are associated with autism spectrum disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.05.24306908. [PMID: 38766206 PMCID: PMC11100849 DOI: 10.1101/2024.05.05.24306908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Coding de novo mutations (DNMs) contribute to the risk for autism spectrum disorders (ASD), but the contribution of noncoding DNMs remains relatively unexplored. Here we use whole genome sequencing (WGS) data of 12,411 individuals (including 3,508 probands and 2,218 unaffected siblings) from 3,357 families collected in Simons Foundation Powering Autism Research for Knowledge (SPARK) to detect DNMs associated with ASD, while examining Simons Simplex Collection (SSC) with 6383 individuals from 2274 families to replicate the results. For coding DNMs, SCN2A reached exome-wide significance (p=2.06×10-11) in SPARK. The 618 known dominant ASD genes as a group are strongly enriched for coding DNMs in cases than sibling controls (fold change=1.51, p =1.13×10-5 for SPARK; fold change=1.86, p =2.06×10-9 for SSC). For noncoding DNMs, we used two methods to assess statistical significance: a point-based test that analyzes sites with a Combined Annotation Dependent Depletion (CADD) score ≥15, and a segment-based test that analyzes 1kb genomic segments with segment-specific background mutation rates (inferred from expected rare mutations in Gnocchi genome constraint scores). The point-based test identified SCN2A as marginally significant (p=6.12×10-4) in SPARK, yet segment-based test identified CSMD1, RBFOX1 and CHD13 as exome-wide significant. We did not identify significant enrichment of noncoding DNMs (in all 1kb segments or those with Gnocchi>4) in the 618 known ASD genes as a group in cases than sibling controls. When combining evidence from both coding and noncoding DNMs, we found that SCN2A with 11 coding and 5 noncoding DNMs exhibited the strongest significance (p=4.15×10-13). In summary, we identified both coding and noncoding DNMs in SCN2A associated with ASD, while nominating additional candidates for further examination in future studies.
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Affiliation(s)
- Yuan Zhang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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20
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Vong KI, Lee S, Au KS, Crowley TB, Capra V, Martino J, Haller M, Araújo C, Machado HR, George R, Gerding B, James KN, Stanley V, Jiang N, Alu K, Meave N, Nidhiry AS, Jiwani F, Tang I, Nisal A, Jhamb I, Patel A, Patel A, McEvoy-Venneri J, Barrows C, Shen C, Ha YJ, Howarth R, Strain M, Ashley-Koch AE, Azam M, Mumtaz S, Bot GM, Finnell RH, Kibar Z, Marwan AI, Melikishvili G, Meltzer HS, Mutchinick OM, Stevenson DA, Mroczkowski HJ, Ostrander B, Schindewolf E, Moldenhauer J, Zackai EH, Emanuel BS, Garcia-Minaur S, Nowakowska BA, Stevenson RE, Zaki MS, Northrup H, McNamara HK, Aldinger KA, Phelps IG, Deng M, Glass IA, Morrow B, McDonald-McGinn DM, Sanna-Cherchi S, Lamb DJ, Gleeson JG. Risk of meningomyelocele mediated by the common 22q11.2 deletion. Science 2024; 384:584-590. [PMID: 38696583 DOI: 10.1126/science.adl1624] [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: 10/08/2023] [Accepted: 03/27/2024] [Indexed: 05/04/2024]
Abstract
Meningomyelocele is one of the most severe forms of neural tube defects (NTDs) and the most frequent structural birth defect of the central nervous system. We assembled the Spina Bifida Sequencing Consortium to identify causes. Exome and genome sequencing of 715 parent-offspring trios identified six patients with chromosomal 22q11.2 deletions, suggesting a 23-fold increased risk compared with the general population. Furthermore, analysis of a separate 22q11.2 deletion cohort suggested a 12- to 15-fold increased NTD risk of meningomyelocele. The loss of Crkl, one of several neural tube-expressed genes within the minimal deletion interval, was sufficient to replicate NTDs in mice, where both penetrance and expressivity were exacerbated by maternal folate deficiency. Thus, the common 22q11.2 deletion confers substantial meningomyelocele risk, which is partially alleviated by folate supplementation.
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Affiliation(s)
- Keng Ioi Vong
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sangmoon Lee
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - T Blaine Crowley
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Valeria Capra
- Genomics and Clinical Genetics Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Meade Haller
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
| | - Camila Araújo
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Hélio R Machado
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Renee George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Bryn Gerding
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kiely N James
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Nan Jiang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kameron Alu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Naomi Meave
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Anna S Nidhiry
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Fiza Jiwani
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Isaac Tang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ashna Nisal
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ishani Jhamb
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Aakash Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Celina Shen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Yoo-Jin Ha
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Robyn Howarth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Madison Strain
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Matloob Azam
- Pediatrics and Child Neurology, Wah Medical College, Wah Cantt, Punjab 47000, Pakistan
| | - Sara Mumtaz
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Punjab 46000, Pakistan
| | - Gyang Markus Bot
- Neurosurgery Division, Department of Surgery, Jos University Teaching Hospital, Jos 930105, Nigeria
| | - Richard H Finnell
- Center for Precision Environmental Health, Departments of Molecular and Human Genetics, Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zoha Kibar
- Department of Neurosciences, University of Montreal and CHU Sainte Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Ahmed I Marwan
- Division of Pediatric Surgery, University of Colorado School of Medicine, Children's Hospital of Colorado, Colorado Fetal Care Center, Aurora, CO 80045, USA
| | - Gia Melikishvili
- Department of Pediatrics, MediClubGeorgia Medical Center, Tbilisi 0160, Georgia
| | - Hal S Meltzer
- Department of Neurosurgery, University of California San Diego, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080 Mexico City, Mexico
| | - David A Stevenson
- Division of Medical Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Henry J Mroczkowski
- Division of Medical Genetics, University of Tennessee Health Science Campus, Memphis, TN 38163, USA
| | - Betsy Ostrander
- Division of Pediatric Neurology, Primary Children's Hospital, University of Utah, Salt Lake City, UT 84113, USA
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julie Moldenhauer
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elaine H Zackai
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beverly S Emanuel
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sixto Garcia-Minaur
- Clinical Genetics Section, Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Beata A Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka, 01-211 Warsaw, Poland
| | - Roger E Stevenson
- JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
| | - Ian G Phelps
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Mei Deng
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Ian A Glass
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Bernice Morrow
- Division of Translational Genetics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Donna M McDonald-McGinn
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Biology and Medical Genetics, Sapienza University, 00185-Rome RM, Italy
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Dolores J Lamb
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
- Department of Urology, Center for Reproductive Genomics, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
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21
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Lu X, Ng K, Pinto E Vairo F, Collins J, Cohn R, Riley K, Agre K, Gavrilova R, Klee EW, Rosenfeld JA, Jiang YH. Novel protein-truncating variants of a chromatin-modifying gene MSL2 in syndromic neurodevelopmental disorders. Eur J Hum Genet 2024:10.1038/s41431-024-01576-0. [PMID: 38702431 DOI: 10.1038/s41431-024-01576-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/04/2023] [Accepted: 02/21/2024] [Indexed: 05/06/2024] Open
Abstract
Numerous large scale genomic studies have uncovered rare but recurrent pathogenetic variants in a significant number of genes encoding epigenetic machinery in cases with neurodevelopmental disorders (NDD) especially autism spectrum disorder (ASD). These findings provide strong support for the functional importance of epigenetic regulators in neurodevelopment. After the clinical genomics evaluation of the patients using exome sequencing, we have identified, three novel protein-truncating variants (PTVs) in the MSL2 gene (OMIM: 614802) which encodes a chromatin modifying enzyme. MSL2 modifies chromatin through both mono-ubiquitination of histone 2B on lysine 34 (K34) and acetylation of histone H4 on lysine 16 (K16). We reported first time the detailed clinical features associated with 3 MSL2 PTVs. There are 15 PTVs (13 de novo) reported from the large genomics studies (12 cases) or ClinVar (3 cases) of NDD, ASD, and developmental disorders (DD) but the specific clinical features for these cases are not described. Taken together, our descriptions of dysmorphic face and other features support the causal role of MSL2 in a likely syndromic neurodevelopmental disorder and add MSL2 to a growing list of epigenetic genes implicated in ASD.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kim Ng
- Pediatric Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Filippo Pinto E Vairo
- Department of Clinical Genomics and Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - James Collins
- Mercy Hospital, Pediatric Neurology, St Louis, MO, USA
| | - Ronald Cohn
- SickKids, The Hospital for Sick Children, 555 University Ave Toronto, Toronto, ON, M5G 1X8, Canada
| | - Kacie Riley
- Pediatric Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Katherine Agre
- Department of Clinical Genomics and Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ralitza Gavrilova
- Department of Clinical Genomics and Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Eric W Klee
- Department of Clinical Genomics and Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77030, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Professor of Genetics, Neuroscience, & Pediatrics Chief of Medical Genetics, Yale University School of Medicine Yale New Haven Hospital, New Haven, CT, 06520, USA.
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22
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Zhong G, Zhao Y, Zhuang D, Chung WK, Shen Y. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581321. [PMID: 38746140 PMCID: PMC11092447 DOI: 10.1101/2024.02.20.581321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenicity classification, but the functional impact of missense variants is multi-dimensional. Pathogenic missense variants in the same gene may act through different modes of action (i.e., gain/loss-of-function) by affecting different aspects of protein function. They may result in distinct clinical conditions that require different treatments. We developed a new method, PreMode, to perform gene-specific mode-of-action predictions. PreMode models effects of coding sequence variants using SE(3)-equivariant graph neural networks on protein sequences and structures. Using the largest-to-date set of missense variants with known modes of action, we showed that PreMode reached state-of-the-art performance in multiple types of mode-of-action predictions by efficient transfer-learning. Additionally, PreMode's prediction of G/LoF variants in a kinase is consistent with inactive-active conformation transition energy changes. Finally, we show that PreMode enables efficient study design of deep mutational scans and optimization in protein engineering.
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23
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Sakaguchi K, Tawata S. Giftedness and atypical sexual differentiation: enhanced perceptual functioning through estrogen deficiency instead of androgen excess. Front Endocrinol (Lausanne) 2024; 15:1343759. [PMID: 38752176 PMCID: PMC11094242 DOI: 10.3389/fendo.2024.1343759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Syndromic autism spectrum conditions (ASC), such as Klinefelter syndrome, also manifest hypogonadism. Compared to the popular Extreme Male Brain theory, the Enhanced Perceptual Functioning model explains the connection between ASC, savant traits, and giftedness more seamlessly, and their co-emergence with atypical sexual differentiation. Overexcitability of primary sensory inputs generates a relative enhancement of local to global processing of stimuli, hindering the abstraction of communication signals, in contrast to the extraordinary local information processing skills in some individuals. Weaker inhibitory function through gamma-aminobutyric acid type A (GABAA) receptors and the atypicality of synapse formation lead to this difference, and the formation of unique neural circuits that process external information. Additionally, deficiency in monitoring inner sensory information leads to alexithymia (inability to distinguish one's own emotions), which can be caused by hypoactivity of estrogen and oxytocin in the interoceptive neural circuits, comprising the anterior insular and cingulate gyri. These areas are also part of the Salience Network, which switches between the Central Executive Network for external tasks and the Default Mode Network for self-referential mind wandering. Exploring the possibility that estrogen deficiency since early development interrupts GABA shift, causing sensory processing atypicality, it helps to evaluate the co-occurrence of ASC with attention deficit hyperactivity disorder, dyslexia, and schizophrenia based on phenotypic and physiological bases. It also provides clues for understanding the common underpinnings of these neurodevelopmental disorders and gifted populations.
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Affiliation(s)
- Kikue Sakaguchi
- Research Department, National Institution for Academic Degrees and Quality Enhancement of Higher Education (NIAD-QE), Kodaira-shi, Tokyo, Japan
| | - Shintaro Tawata
- Graduate School of Human Sciences, Sophia University, Chiyoda-ku, Tokyo, Japan
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24
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Jensen HH, Olsen A. Neurological consequences of human calmodulin mutations. Neural Regen Res 2024; 19:943-944. [PMID: 37862180 PMCID: PMC10749624 DOI: 10.4103/1673-5374.385299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 10/22/2023] Open
Affiliation(s)
- Helene H. Jensen
- Medical Biotechnology, Department of Chemistry and Biosciences, Aalborg University, Aalborg, Denmark
| | - Anders Olsen
- Medical Biotechnology, Department of Chemistry and Biosciences, Aalborg University, Aalborg, Denmark
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25
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Wang C, Derderian KD, Hamada E, Zhou X, Nelson AD, Kyoung H, Ahituv N, Bouvier G, Bender KJ. Impaired cerebellar plasticity hypersensitizes sensory reflexes in SCN2A-associated ASD. Neuron 2024; 112:1444-1455.e5. [PMID: 38412857 PMCID: PMC11065582 DOI: 10.1016/j.neuron.2024.01.029] [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: 05/22/2023] [Revised: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
Children diagnosed with autism spectrum disorder (ASD) commonly present with sensory hypersensitivity or abnormally strong reactions to sensory stimuli. Such hypersensitivity can be overwhelming, causing high levels of distress that contribute markedly to the negative aspects of the disorder. Here, we identify a mechanism that underlies hypersensitivity in a sensorimotor reflex found to be altered in humans and in mice with loss of function in the ASD risk-factor gene SCN2A. The cerebellum-dependent vestibulo-ocular reflex (VOR), which helps maintain one's gaze during movement, was hypersensitized due to deficits in cerebellar synaptic plasticity. Heterozygous loss of SCN2A-encoded NaV1.2 sodium channels in granule cells impaired high-frequency transmission to Purkinje cells and long-term potentiation, a form of synaptic plasticity important for modulating VOR gain. VOR plasticity could be rescued in mice via a CRISPR-activator approach that increases Scn2a expression, demonstrating that evaluation of a simple reflex can be used to assess and quantify successful therapeutic intervention.
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Affiliation(s)
- Chenyu Wang
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kimberly D Derderian
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Elizabeth Hamada
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew D Nelson
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Henry Kyoung
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Guy Bouvier
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA; Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91400 Saclay, France.
| | - Kevin J Bender
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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26
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Bouman A, Geelen JM, Kummeling J, Schenck A, van der Zwan YG, Klein WM, Kleefstra T. Growth, body composition, and endocrine-metabolic profiles of individuals with Kleefstra syndrome provide directions for clinical management and translational studies. Am J Med Genet A 2024; 194:e63472. [PMID: 38155610 DOI: 10.1002/ajmg.a.63472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/17/2023] [Accepted: 10/27/2023] [Indexed: 12/30/2023]
Abstract
Mendelian neurodevelopmental disorders caused by variants in genes encoding chromatin modification can be categorized as Mendelian disorders of the epigenetic machinery (MDEMs). These disorders have significant overlap in molecular pathways and phenotypes including intellectual disability, short stature, and obesity. Among the MDEMs is Kleefstra syndrome (KLFS), which is caused by haploinsufficiency of EHMT1. Preclinical studies have identified metabolic dysregulation and obesity in KLFS models, but proper clinical translation lacks. In this study, we aim to delineate growth, body composition, and endocrine-metabolic characteristics in a total of 62 individuals with KLFS. Our results revealed a high prevalence of childhood-onset overweight/obesity (60%; 28/47) with disproportionately high body fat percentage, which aligns perfectly with previous preclinical studies. Short stature was common (33%), likely due to advanced skeletal maturation. Endocrine-metabolic investigations showed thyroid dysregulation (22%; 9/41), elevated triglycerides, and decreased blood ammonia levels. Moreover, hand radiographs identified decreased bone mineralization (57%; 8/14) and negative ulnar variance (71%; 10/14). Our findings indicate a high (cardio)metabolic risk in KLFS. Therefore, we recommend monitoring of weight and endocrine-metabolic profile. Supporting a healthy lifestyle and screening of bone mineralization is advised. Our comprehensive results support translational research and contribute to a better understanding of MDEM-associated phenotypes.
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Affiliation(s)
- Arianne Bouman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joyce M Geelen
- Department of Pediatrics, Developmental and Genetic Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost Kummeling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annette Schenck
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yvonne G van der Zwan
- Department of Pediatrics, Pediatric Endocrinology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willemijn M Klein
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands
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27
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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28
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Hizawa K, Sasaki T, Arimura N. A comparative overview of DSCAM and its multifunctional roles in Drosophila and vertebrates. Neurosci Res 2024; 202:1-7. [PMID: 38141781 DOI: 10.1016/j.neures.2023.12.005] [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: 10/19/2023] [Revised: 11/21/2023] [Accepted: 12/14/2023] [Indexed: 12/25/2023]
Abstract
DSCAM (Down syndrome cell adhesion molecule) is a unique neuronal adhesion protein with extensively documented multifaceted functionalities. DSCAM also has interesting properties in vertebrates and invertebrates, respectively. In Drosophila species, particularly, Dscam exhibits remarkable genetic diversity, with tens of thousands of splicing isoforms that modulate the specificity of neuronal wiring. Interestingly, this splice variant diversity of Dscam is absent in vertebrates. DSCAM plays a pivotal role in mitigating excessive adhesion between identical cell types, thereby maintaining the structural and functional coherence of neural networks. DSCAM contributes to the oversight of selective intercellular interactions such as synaptogenesis; however, the precise regulatory mechanisms underlying the promotion and inhibition of cell adhesion involved remain unclear. In this review, we aim to delineate the distinct molecules that interact with DSCAM and their specific roles within the biological landscapes of Drosophila and vertebrates. By integrating these comparative insights, we aim to elucidate the multifunctional nature of DSCAM, particularly its capacity to facilitate or deter intercellular adhesion.
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Affiliation(s)
- Kento Hizawa
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8578, Japan
| | - Takuya Sasaki
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8578, Japan
| | - Nariko Arimura
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8578, Japan.
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29
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Sudnawa KK, Garber A, Cohen R, Calamia S, Kanner CH, Montes J, Bain JM, Fee RJ, Chung WK. Clinical phenotypic spectrum of CTNNB1 neurodevelopmental disorder. Clin Genet 2024; 105:523-532. [PMID: 38247296 DOI: 10.1111/cge.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Pathogenic heterozygous loss of function variants in CTNNB1 are associated with CTNNB1 neurodevelopmental disorder. We report the clinical phenotype of individuals with CTNNB1 neurodevelopmental disorder using both caregiver-reported data (medical history, adaptive function, quality of life, and behavior issues) and in-person clinical assessments (neurological, motor, and cognitive function) in 32 individuals with likely pathogenic or pathogenic CTNNB1 variants. Most individuals had truncal hypotonia, muscle weakness, hypertonia, dystonia, microcephaly, and many had a history of tethered cord. Visual problems included strabismus, hyperopia, and familial exudative vitreoretinopathy. Half of individuals walked without an assistive device. The mean Gross Motor Functional Measure-66 score was 56.6 (SD = 14.8). Average time to complete Nine-Hole Peg Test was slower than norms. Mean general conceptual ability composite scores from Differential Ability Scales Second Edition were very low (M = 58.3, SD = 11.3). Fifty-five percent of individuals had low adaptive functioning based on the Vineland Adaptive Behavioral Scales. Based upon the Child Behavior Checklist total problems score, the majority (65%) of individuals had behavioral challenges. The mean overall Quality of Life Inventory-Disability score was 81.7 (SD = 11.9). These data provide a detailed characterization of clinical features in individuals with CTNNB1 neurodevelopmental disorder.
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Affiliation(s)
- Khemika K Sudnawa
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Pramongkutklao Hospital and Pramongkutklao College of Medicine, Bangkok, Thailand
| | - Alison Garber
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Ryan Cohen
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Sean Calamia
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Cara H Kanner
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jacqueline Montes
- Department of Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer M Bain
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Robert J Fee
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Hospital, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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30
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Priyanka P, Gopalakrishnan AP, Nisar M, Shivamurthy PB, George M, John L, Sanjeev D, Yandigeri T, Thomas SD, Rafi A, Dagamajalu S, Velikkakath AKG, Abhinand CS, Kanekar S, Prasad TSK, Balaya RDA, Raju R. A global phosphosite-correlated network map of Thousand And One Kinase 1 (TAOK1). Int J Biochem Cell Biol 2024; 170:106558. [PMID: 38479581 DOI: 10.1016/j.biocel.2024.106558] [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: 08/12/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
Thousand and one amino acid kinase 1 (TAOK1) is a sterile 20 family Serine/Threonine kinase linked to microtubule dynamics, checkpoint signaling, DNA damage response, and neurological functions. Molecular-level alterations of TAOK1 have been associated with neurodevelopment disorders and cancers. Despite their known involvement in physiological and pathophysiological processes, and as a core member of the hippo signaling pathway, the phosphoregulatory network of TAOK1 has not been visualized. Aimed to explore this network, we first analyzed the predominantly detected and differentially regulated TAOK1 phosphosites in global phosphoproteome datasets across diverse experimental conditions. Based on 709 qualitative and 210 quantitative differential cellular phosphoproteome datasets that were systematically assembled, we identified that phosphorylation at Ser421, Ser9, Ser965, and Ser445 predominantly represented TAOK1 in almost 75% of these datasets. Surprisingly, the functional role of all these phosphosites in TAOK1 remains unexplored. Hence, we employed a robust strategy to extract the phosphosites in proteins that significantly correlated in expression with predominant TAOK1 phosphosites. This led to the first categorization of the phosphosites including those in the currently known and predicted interactors, kinases, and substrates, that positively/negatively correlated with the expression status of each predominant TAOK1 phosphosites. Subsequently, we also analyzed the phosphosites in core proteins of the hippo signaling pathway. Based on the TAOK1 phosphoregulatory network analysis, we inferred the potential role of the predominant TAOK1 phosphosites. Especially, we propose pSer9 as an autophosphorylation and TAOK1 kinase activity-associated phosphosite and pS421, the most frequently detected phosphosite in TAOK1, as a significant regulatory phosphosite involved in the maintenance of genome integrity. Considering that the impact of all phosphosites that predominantly represent each kinase is essential for the efficient interpretation of global phosphoproteome datasets, we believe that the approach undertaken in this study is suitable to be extended to other kinases for accelerated research.
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Affiliation(s)
- Pahal Priyanka
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Athira Perunelly Gopalakrishnan
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | - Mejo George
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Tanuja Yandigeri
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Sonet D Thomas
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Ahmad Rafi
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Anoop Kumar G Velikkakath
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Chandran S Abhinand
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Saptami Kanekar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | | | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
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31
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Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [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: 05/30/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
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Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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32
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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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33
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Chardon FM, McDiarmid TA, Page NF, Daza RM, Martin B, Domcke S, Regalado SG, Lalanne JB, Calderon D, Li X, Starita LM, Sanders SJ, Ahituv N, Shendure J. Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.28.534017. [PMID: 37034704 PMCID: PMC10081248 DOI: 10.1101/2023.03.28.534017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
CRISPR-based gene activation (CRISPRa) is a promising therapeutic approach for gene therapy, upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis- regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis- regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additional trans- acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate therapeutically relevant genes in a cell type-specific manner.
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Vilela J, Rasga C, Santos JX, Martiniano H, Marques AR, Oliveira G, Vicente AM. Bridging Genetic Insights with Neuroimaging in Autism Spectrum Disorder-A Systematic Review. Int J Mol Sci 2024; 25:4938. [PMID: 38732157 PMCID: PMC11084239 DOI: 10.3390/ijms25094938] [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: 02/29/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Autism Spectrum Disorder (ASD) is an early onset neurodevelopmental disorder characterized by impaired social interaction and communication, and repetitive patterns of behavior. Family studies show that ASD is highly heritable, and hundreds of genes have previously been implicated in the disorder; however, the etiology is still not fully clear. Brain imaging and electroencephalography (EEG) are key techniques that study alterations in brain structure and function. Combined with genetic analysis, these techniques have the potential to help in the clarification of the neurobiological mechanisms contributing to ASD and help in defining novel therapeutic targets. To further understand what is known today regarding the impact of genetic variants in the brain alterations observed in individuals with ASD, a systematic review was carried out using Pubmed and EBSCO databases and following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. This review shows that specific genetic variants and altered patterns of gene expression in individuals with ASD may have an effect on brain circuits associated with face processing and social cognition, and contribute to excitation-inhibition imbalances and to anomalies in brain volumes.
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Affiliation(s)
- Joana Vilela
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (C.R.); (J.X.S.); (H.M.); (A.R.M.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Célia Rasga
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (C.R.); (J.X.S.); (H.M.); (A.R.M.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - João Xavier Santos
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (C.R.); (J.X.S.); (H.M.); (A.R.M.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Hugo Martiniano
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (C.R.); (J.X.S.); (H.M.); (A.R.M.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Ana Rita Marques
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (C.R.); (J.X.S.); (H.M.); (A.R.M.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo, Serviço do Centro de Desenvolvimento da Criança, Centro de Investigação e Formação Clínica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra (CHUC), 3000-602 Coimbra, Portugal;
- Coimbra Institute for Biomedical Imaging and Translational Research, University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
| | - Astrid Moura Vicente
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (C.R.); (J.X.S.); (H.M.); (A.R.M.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
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Pérez-Cano L, Boccuto L, Sirci F, Hidalgo JM, Valentini S, Bosio M, Liogier D’Ardhuy X, Skinner C, Cascio L, Srikanth S, Jones K, Buchanan CB, Skinner SA, Gomez-Mancilla B, Hyvelin JM, Guney E, Durham L. Characterization of a Clinically and Biologically Defined Subgroup of Patients with Autism Spectrum Disorder and Identification of a Tailored Combination Treatment. Biomedicines 2024; 12:991. [PMID: 38790952 PMCID: PMC11117897 DOI: 10.3390/biomedicines12050991] [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: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental disorders (NDDs) with a high unmet medical need. The diagnosis of ASD is currently based on behavior criteria, which overlooks the diversity of genetic, neurophysiological, and clinical manifestations. Failure to acknowledge such heterogeneity has hindered the development of efficient drug treatments for ASD and other NDDs. DEPI® (Databased Endophenotyping Patient Identification) is a systems biology, multi-omics, and machine learning-driven platform enabling the identification of subgroups of patients with NDDs and the development of patient-tailored treatments. In this study, we provide evidence for the validation of a first clinically and biologically defined subgroup of patients with ASD identified by DEPI, ASD Phenotype 1 (ASD-Phen1). Among 313 screened patients with idiopathic ASD, the prevalence of ASD-Phen1 was observed to be ~24% in 84 patients who qualified to be enrolled in the study. Metabolic and transcriptomic alterations differentiating patients with ASD-Phen1 were consistent with an over-activation of NF-κB and NRF2 transcription factors, as predicted by DEPI. Finally, the suitability of STP1 combination treatment to revert such observed molecular alterations in patients with ASD-Phen1 was determined. Overall, our results support the development of precision medicine-based treatments for patients diagnosed with ASD.
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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; (F.S.); (J.M.H.); (S.V.); (M.B.); (E.G.)
| | - Luigi Boccuto
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29649, USA; (L.B.); (C.S.); (L.C.); (S.S.); (K.J.); (C.B.B.); (S.A.S.)
- Healthcare Genetics and Genomics, School of Nursing, Clemson University, Clemson, SC 29634, USA
| | - Francesco Sirci
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; (F.S.); (J.M.H.); (S.V.); (M.B.); (E.G.)
| | - Jose Manuel Hidalgo
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; (F.S.); (J.M.H.); (S.V.); (M.B.); (E.G.)
| | - Samuel Valentini
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; (F.S.); (J.M.H.); (S.V.); (M.B.); (E.G.)
| | - Mattia Bosio
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; (F.S.); (J.M.H.); (S.V.); (M.B.); (E.G.)
| | - Xavier Liogier D’Ardhuy
- Drug Development Unit (DDU), STALICLA SA, Avenue de Sécheron 15, 1202 Geneva, Switzerland; (X.L.D.); (B.G.-M.); (J.-M.H.)
| | - Cindy Skinner
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29649, USA; (L.B.); (C.S.); (L.C.); (S.S.); (K.J.); (C.B.B.); (S.A.S.)
| | - Lauren Cascio
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29649, USA; (L.B.); (C.S.); (L.C.); (S.S.); (K.J.); (C.B.B.); (S.A.S.)
- Research and Education in Disease Diagnosis and Interventions (REDDI) Lab, Center for Innovative Medical Devices and Sensors (CIMeDS), Clemson University, Clemson, SC 29634, USA
| | - Sujata Srikanth
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29649, USA; (L.B.); (C.S.); (L.C.); (S.S.); (K.J.); (C.B.B.); (S.A.S.)
- Research and Education in Disease Diagnosis and Interventions (REDDI) Lab, Center for Innovative Medical Devices and Sensors (CIMeDS), Clemson University, Clemson, SC 29634, USA
| | - Kelly Jones
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29649, USA; (L.B.); (C.S.); (L.C.); (S.S.); (K.J.); (C.B.B.); (S.A.S.)
- Research and Education in Disease Diagnosis and Interventions (REDDI) Lab, Center for Innovative Medical Devices and Sensors (CIMeDS), Clemson University, Clemson, SC 29634, USA
| | - Caroline B. Buchanan
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29649, USA; (L.B.); (C.S.); (L.C.); (S.S.); (K.J.); (C.B.B.); (S.A.S.)
| | - Steven A. Skinner
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29649, USA; (L.B.); (C.S.); (L.C.); (S.S.); (K.J.); (C.B.B.); (S.A.S.)
| | - Baltazar Gomez-Mancilla
- Drug Development Unit (DDU), STALICLA SA, Avenue de Sécheron 15, 1202 Geneva, Switzerland; (X.L.D.); (B.G.-M.); (J.-M.H.)
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 0G4, Canada
| | - Jean-Marc Hyvelin
- Drug Development Unit (DDU), STALICLA SA, Avenue de Sécheron 15, 1202 Geneva, Switzerland; (X.L.D.); (B.G.-M.); (J.-M.H.)
| | - Emre Guney
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; (F.S.); (J.M.H.); (S.V.); (M.B.); (E.G.)
| | - Lynn Durham
- Discovery and Data Science (DDS) Unit, STALICLA SL, Moll de Barcelona, s/n, Edif Este, 08039 Barcelona, Spain; (F.S.); (J.M.H.); (S.V.); (M.B.); (E.G.)
- Drug Development Unit (DDU), STALICLA SA, Avenue de Sécheron 15, 1202 Geneva, Switzerland; (X.L.D.); (B.G.-M.); (J.-M.H.)
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West KL, Kreiling N, Raney KD, Ghosal G, Leung JW. Autophosphorylation of the Tousled-like kinases TLK1 and TLK2 regulates recruitment to damaged chromatin via PCNA interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590659. [PMID: 38712247 PMCID: PMC11071368 DOI: 10.1101/2024.04.22.590659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tousled-like kinases 1 and 2 (TLK1 and 2) are cell cycle-regulated serine/threonine kinases that are involved in multiple biological processes. Mutation of TLK1 and 2 confer neurodegenerative diseases. Recent studies demonstrate that TLK1 and 2 are involved in DNA repair. However, there is no direct evidence that TLK1 and 2 function at DNA damage sites. Here, we show that both TLK1 and TLK2 are hyper-autophosphorylated at their N-termini, at least in part, mediated by their homo- or hetero-dimerization. We found that TLK1 and 2 hyper-autophosphorylation suppresses their recruitment to damaged chromatin. Furthermore, both TLK1 and 2 associate with PCNA specifically through their evolutionarily conserved non-canonical PCNA-interacting protein (PIP) box at the N-terminus, and mutation of the PIP-box abolishes their recruitment to DNA damage sites. Mechanistically, the TLK1 and 2 hyper-autophosphorylation masks the PIP-box and negatively regulates their recruitment to the DNA damage site. Overall, our study dissects the detailed genetic regulation of TLK1 and 2 at damaged chromatin, which provides important insights into their emerging roles in DNA repair.
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Affiliation(s)
- Kirk L. West
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Natasha Kreiling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Kevin D. Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Justin W Leung
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
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Kastner DB, Williams G, Holobetz C, Romano JP, Dayan P. The choice-wide behavioral association study: data-driven identification of interpretable behavioral components. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582115. [PMID: 38464037 PMCID: PMC10925091 DOI: 10.1101/2024.02.26.582115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Behavior contains rich structure across many timescales, but there is a dearth of methods to identify relevant components, especially over the longer periods required for learning and decision-making. Inspired by the goals and techniques of genome-wide association studies, we present a data-driven method-the choice-wide behavioral association study: CBAS-that systematically identifies such behavioral features. CBAS uses a powerful, resampling-based, method of multiple comparisons correction to identify sequences of actions or choices that either differ significantly between groups or significantly correlate with a covariate of interest. We apply CBAS to different tasks and species (flies, rats, and humans) and find, in all instances, that it provides interpretable information about each behavioral task.
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Affiliation(s)
- David B. Kastner
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
- Lead Contact
| | - Greer Williams
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
| | - Cristofer Holobetz
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
| | - Joseph P. Romano
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Peter Dayan
- Max Planck Institute for Biological Cybernetics, Tübingen 72076, Germany
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Privitera F, Pagano S, Meossi C, Battini R, Bartolini E, Montanaro D, Santorelli FM. Non-Specific Epileptic Activity, EEG, and Brain Imaging in Loss of Function Variants in SATB1: A New Case Report and Review of the Literature. Genes (Basel) 2024; 15:548. [PMID: 38790177 PMCID: PMC11120869 DOI: 10.3390/genes15050548] [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: 04/06/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
SATB1 (MIM #602075) is a relatively new gene reported only in recent years in association with neurodevelopmental disorders characterized by variable facial dysmorphisms, global developmental delay, poor or absent speech, altered electroencephalogram (EEG), and brain abnormalities on imaging. To date about thirty variants in forty-four patients/children have been described, with a heterogeneous spectrum of clinical manifestations. In the present study, we describe a new patient affected by mild intellectual disability, speech disorder, and non-specific abnormalities on EEG and neuroimaging. Family studies identified a new de novo frameshift variant c.1818delG (p.(Gln606Hisfs*101)) in SATB1. To better define genotype-phenotype associations in the different types of reported SATB1 variants, we reviewed clinical data from our patient and from the literature and compared manifestations (epileptic activity, EEG abnormalities and abnormal brain imaging) due to missense variants versus those attributable to loss-of-function/premature termination variants. Our analyses showed that the latter variants are associated with less severe, non-specific clinical features when compared with the more severe phenotypes due to missense variants. These findings provide new insights into SATB1-related disorders.
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Affiliation(s)
- Flavia Privitera
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Via dei Giacinti 2, 56128 Pisa, Italy; (F.P.); (S.P.); (C.M.); (R.B.); (E.B.)
- Molecular Medicine, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
| | - Stefano Pagano
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Via dei Giacinti 2, 56128 Pisa, Italy; (F.P.); (S.P.); (C.M.); (R.B.); (E.B.)
- Molecular Medicine, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
- Medical Genetics, Residency Program, Federico II University, Via S. Pansini 5, 80131 Naples, Italy
| | - Camilla Meossi
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Via dei Giacinti 2, 56128 Pisa, Italy; (F.P.); (S.P.); (C.M.); (R.B.); (E.B.)
- Molecular Medicine, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Via dei Giacinti 2, 56128 Pisa, Italy; (F.P.); (S.P.); (C.M.); (R.B.); (E.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Emanuele Bartolini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Via dei Giacinti 2, 56128 Pisa, Italy; (F.P.); (S.P.); (C.M.); (R.B.); (E.B.)
- Tuscany PhD Program in Neurosciences, 50139 Florence, Italy
| | - Domenico Montanaro
- U.O.S. Dipartimentale e Servizio Autonomo di Risonanza Magnetica, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Filippo Maria Santorelli
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Via dei Giacinti 2, 56128 Pisa, Italy; (F.P.); (S.P.); (C.M.); (R.B.); (E.B.)
- Molecular Medicine, IRCCS Fondazione Stella Maris, Via dei Giacinti 2, 56128 Pisa, Italy
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Bhattacharya A, Parlanti P, Cavallo L, Farrow E, Spivey T, Renieri A, Mari F, Manzini MC. A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A. Hum Mol Genet 2024:ddae070. [PMID: 38652285 DOI: 10.1093/hmg/ddae070] [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: 11/30/2023] [Revised: 03/07/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous with hundreds of identified risk genes, most affecting only a few patients. Novel missense variants in these genes are being discovered as clinical exome sequencing is now routinely integrated into diagnosis, yet most of them are annotated as variants of uncertain significance (VUS). VUSs are a major roadblock in using patient genetics to inform clinical action. We developed a framework to characterize VUSs in Coiled-coil and C2 domain containing 1A (CC2D1A), a gene causing autosomal recessive ID with comorbid ASD in 40% of cases. We analyzed seven VUSs (p.Pro319Leu, p.Ser327Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, p.Arg886His and p.Glu910Lys) from four cases of individuals with ID and ASD. Variants were cloned and overexpressed in HEK293 individually and in their respective heterozygous combination. CC2D1A is a signaling scaffold that positively regulates PKA-CREB signaling by repressing phosphodiesterase 4D (PDE4D) to prevent cAMP degradation. After testing multiple parameters including direct interaction between PDE4D and CC2D1A, cAMP levels and CREB activation, we found that the most sensitive readout was CREB transcriptional activity using a luciferase assay. Compared to WT CC2D1A, five VUSs (p.Pro319Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, and p.Arg886His) led to significantly blunted response to forskolin induced CREB activation. This luciferase assay approach can be scaled up to annotate ~150 CC2D1A VUSs that are currently listed in ClinVar. Since CREB activation is a common denominator for multiple ASD/ID genes, our paradigm can also be adapted for their VUSs.
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Affiliation(s)
- Aniket Bhattacharya
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Paola Parlanti
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Luca Cavallo
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Edward Farrow
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Tyler Spivey
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - M Chiara Manzini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
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Carlton AJ, Jeng JY, Grandi FC, De Faveri F, Amariutei AE, De Tomasi L, O'Connor A, Johnson SL, Furness DN, Brown SDM, Ceriani F, Bowl MR, Mustapha M, Marcotti W. BAI1 localizes AMPA receptors at the cochlear afferent post-synaptic density and is essential for hearing. Cell Rep 2024; 43:114025. [PMID: 38564333 DOI: 10.1016/j.celrep.2024.114025] [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: 09/14/2023] [Revised: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Type I spiral ganglion neurons (SGNs) convey sound information to the central auditory pathway by forming synapses with inner hair cells (IHCs) in the mammalian cochlea. The molecular mechanisms regulating the formation of the post-synaptic density (PSD) in the SGN afferent terminals are still unclear. Here, we demonstrate that brain-specific angiogenesis inhibitor 1 (BAI1) is required for the clustering of AMPA receptors GluR2-4 (glutamate receptors 2-4) at the PSD. Adult Bai1-deficient mice have functional IHCs but fail to transmit information to the SGNs, leading to highly raised hearing thresholds. Despite the almost complete absence of AMPA receptor subunits, the SGN fibers innervating the IHCs do not degenerate. Furthermore, we show that AMPA receptors are still expressed in the cochlea of Bai1-deficient mice, highlighting a role for BAI1 in trafficking or anchoring GluR2-4 to the PSDs. These findings identify molecular and functional mechanisms required for sound encoding at cochlear ribbon synapses.
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Affiliation(s)
- Adam J Carlton
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jing-Yi Jeng
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Fiorella C Grandi
- Sorbonne Université, INSERM, Institute de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | | | - Ana E Amariutei
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Lara De Tomasi
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Andrew O'Connor
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Stuart L Johnson
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Sheffield S10 2TN, UK
| | - David N Furness
- School of Life Sciences, Keele University, Keele ST5 5BG, UK
| | - Steve D M Brown
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Federico Ceriani
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael R Bowl
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Mirna Mustapha
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Sheffield S10 2TN, UK
| | - Walter Marcotti
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Sheffield S10 2TN, UK.
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41
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Delling JP, Bauer HF, Gerlach-Arbeiter S, Schön M, Jacob C, Wagner J, Pedro MT, Knöll B, Boeckers TM. Combined expansion and STED microscopy reveals altered fingerprints of postsynaptic nanostructure across brain regions in ASD-related SHANK3-deficiency. Mol Psychiatry 2024:10.1038/s41380-024-02559-9. [PMID: 38649753 DOI: 10.1038/s41380-024-02559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Synaptic dysfunction is a key feature of SHANK-associated disorders such as autism spectrum disorder, schizophrenia, and Phelan-McDermid syndrome. Since detailed knowledge of their effect on synaptic nanostructure remains limited, we aimed to investigate such alterations in ex11|SH3 SHANK3-KO mice combining expansion and STED microscopy. This enabled high-resolution imaging of mosaic-like arrangements formed by synaptic proteins in both human and murine brain tissue. We found distinct shape-profiles as fingerprints of the murine postsynaptic scaffold across brain regions and genotypes, as well as alterations in the spatial and molecular organization of subsynaptic domains under SHANK3-deficient conditions. These results provide insights into synaptic nanostructure in situ and advance our understanding of molecular mechanisms underlying synaptic dysfunction in neuropsychiatric disorders.
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Affiliation(s)
- Jan Philipp Delling
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany.
- Max Planck Institute of Psychiatry, Munich, 80804, Germany.
| | | | | | - Michael Schön
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany
| | - Christian Jacob
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany
| | - Jan Wagner
- Department of Neurology, Ulm University, Ulm, 89081, Germany
| | | | - Bernd Knöll
- Institute of Neurobiochemistry, Ulm University, Ulm, 89081, Germany
| | - Tobias M Boeckers
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany.
- Ulm Site, DZNE, Ulm, 89081, Germany.
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Koko M, Kyle Satterstrom F, Warrier V, Martin H. Contribution of autosomal rare and de novo variants to sex differences in autism. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.13.24305713. [PMID: 38699304 PMCID: PMC11065020 DOI: 10.1101/2024.04.13.24305713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Autism is four times more prevalent in males than females. To study whether this reflects a difference in genetic predisposition attributed to autosomal rare variants, we evaluated the sex differences in effect size of damaging protein-truncating and missense variants on autism predisposition in 47,061 autistic individuals, then compared effect sizes between individuals with and without cognitive impairment or motor delay. Although these variants mediated differential likelihood of autism with versus without motor or cognitive impairment, their effect sizes on the liability scale did not differ significantly by sex exome-wide or in genes sex-differentially expressed in the cortex. Although de novo mutations were enriched in genes with male-biased expression in the fetal cortex, the liability they conferred did not differ significantly from other genes with similar loss-of-function intolerance and sex-averaged cortical expression. In summary, autosomal rare coding variants confer similar liability for autism in females and males.
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Affiliation(s)
- Mahmoud Koko
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - F. Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Varun Warrier
- Department of Psychiatry, Autism Research Centre, University of Cambridge, Cambridge, Cambridgeshire, CB2 8AH, UK
| | - Hilary Martin
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
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43
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Goodkey K, Wischmeijer A, Perrin L, Watson AES, Qureshi L, Cordelli DM, Toni F, Gnazzo M, Benedicenti F, Elmaleh-Bergès M, Low KJ, Voronova A. Olfactory bulb anomalies in KBG syndrome mouse model and patients. BMC Med 2024; 22:158. [PMID: 38616269 PMCID: PMC11017579 DOI: 10.1186/s12916-024-03363-6] [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: 08/02/2023] [Accepted: 03/18/2024] [Indexed: 04/16/2024] Open
Abstract
ANKRD11 (ankyrin repeat domain 11) is a chromatin regulator and the only gene associated with KBG syndrome, a rare neurodevelopmental disorder. We have previously shown that Ankrd11 regulates murine embryonic cortical neurogenesis. Here, we show a novel olfactory bulb phenotype in a KBG syndrome mouse model and two diagnosed patients. Conditional knockout of Ankrd11 in murine embryonic neural stem cells leads to aberrant postnatal olfactory bulb development and reduced size due to reduction of the olfactory bulb granule cell layer. We further show that the rostral migratory stream has incomplete migration of neuroblasts, reduced cell proliferation as well as aberrant differentiation of neurons. This leads to reduced neuroblasts and neurons in the olfactory bulb granule cell layer. In vitro, Ankrd11-deficient neural stem cells from the postnatal subventricular zone display reduced migration, proliferation, and neurogenesis. Finally, we describe two clinically and molecularly confirmed KBG syndrome patients with anosmia and olfactory bulb and groove hypo-dysgenesis/agenesis. Our report provides evidence that Ankrd11 is a novel regulator of olfactory bulb development and neuroblast migration. Moreover, our study highlights a novel clinical sign of KBG syndrome linked to ANKRD11 perturbations in mice and humans.
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Affiliation(s)
- Kara Goodkey
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Women and Children's Health Research Institute, University of Alberta, 5-083 Edmonton Clinic Health Academy, Edmonton, AB, T6G 1C9, Canada
| | - Anita Wischmeijer
- Clinical Genetics Service and Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Adrianne E S Watson
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Women and Children's Health Research Institute, University of Alberta, 5-083 Edmonton Clinic Health Academy, Edmonton, AB, T6G 1C9, Canada
| | - Leenah Qureshi
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Duccio Maria Cordelli
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, UOC Neuropsichiatria Dell'età Pediatrica, Bologna, Italy
| | - Francesco Toni
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, Programma Di Neuroradiologia Con Tecniche Ad Elevata Complessità (PNTEC), Bologna, Italy
| | - Maria Gnazzo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00165, Rome, Italy
| | - Francesco Benedicenti
- Clinical Genetics Service and Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Karen J Low
- Department of Academic Child Health, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
- Clinical Genetics Service, St. Michaels Hospital, Bristol, UK
| | - Anastassia Voronova
- Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
- Women and Children's Health Research Institute, University of Alberta, 5-083 Edmonton Clinic Health Academy, Edmonton, AB, T6G 1C9, Canada.
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
- Faculty of Medicine & Dentistry, Neuroscience and Mental Health Institute, Edmonton, AB, T6G 2E1, Canada.
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Neuhaus E, Rea H, Jones E, Benavidez H, Miles C, Whiting A, Johansson M, Eayrs C, Kurtz-Nelson EC, Earl R, Bernier RA, Eichler EE. Shared and divergent mental health characteristics of ADNP-, CHD8- and DYRK1A-related neurodevelopmental conditions. J Neurodev Disord 2024; 16:15. [PMID: 38622540 PMCID: PMC11017562 DOI: 10.1186/s11689-024-09532-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Neurodevelopmental conditions such as intellectual disability (ID) and autism spectrum disorder (ASD) can stem from a broad array of inherited and de novo genetic differences, with marked physiological and behavioral impacts. We currently know little about the psychiatric phenotypes of rare genetic variants associated with ASD, despite heightened risk of psychiatric concerns in ASD more broadly. Understanding behavioral features of these variants can identify shared versus specific phenotypes across gene groups, facilitate mechanistic models, and provide prognostic insights to inform clinical practice. In this paper, we evaluate behavioral features within three gene groups associated with ID and ASD - ADNP, CHD8, and DYRK1A - with two aims: (1) characterize phenotypes across behavioral domains of anxiety, depression, ADHD, and challenging behavior; and (2) understand whether age and early developmental milestones are associated with later mental health outcomes. METHODS Phenotypic data were obtained for youth with disruptive variants in ADNP, CHD8, or DYRK1A (N = 65, mean age = 8.7 years, 40% female) within a long-running, genetics-first study. Standardized caregiver-report measures of mental health features (anxiety, depression, attention-deficit/hyperactivity, oppositional behavior) and developmental history were extracted and analyzed for effects of gene group, age, and early developmental milestones on mental health features. RESULTS Patterns of mental health features varied by group, with anxiety most prominent for CHD8, oppositional features overrepresented among ADNP, and attentional and depressive features most prominent for DYRK1A. For the full sample, age was positively associated with anxiety features, such that elevations in anxiety relative to same-age and same-sex peers may worsen with increasing age. Predictive utility of early developmental milestones was limited, with evidence of early language delays predicting greater difficulties across behavioral domains only for the CHD8 group. CONCLUSIONS Despite shared associations with autism and intellectual disability, disruptive variants in ADNP, CHD8, and DYRK1A may yield variable psychiatric phenotypes among children and adolescents. With replication in larger samples over time, efforts such as these may contribute to improved clinical care for affected children and adolescents, allow for earlier identification of emerging mental health difficulties, and promote early intervention to alleviate concerns and improve quality of life.
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Affiliation(s)
- Emily Neuhaus
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Center On Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, WA, USA.
| | - Hannah Rea
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Elizabeth Jones
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah Benavidez
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Conor Miles
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alana Whiting
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Margaret Johansson
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Curtis Eayrs
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Rachel Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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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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46
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Luo T, Pan J, Zhu Y, Wang X, Li K, Zhao G, Li B, Hu Z, Xia K, Li J. Association between de novo variants of nuclear-encoded mitochondrial-related genes and undiagnosed developmental disorder and autism. QJM 2024; 117:269-276. [PMID: 37930872 PMCID: PMC11014680 DOI: 10.1093/qjmed/hcad249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Evidence suggests that mitochondrial abnormalities increase the risk of two neurodevelopmental disorders: undiagnosed developmental disorder (UDD) and autism spectrum disorder (ASD). However, which nuclear-encoded mitochondrial-related genes (NEMGs) were associated with UDD-ASD is unclear. AIM To explore the association between de novo variants (DNVs) of NEMGs and UDD-ASD. DESIGN Comprehensive analysis based on DNVs of NEMGs identified in patients (31 058 UDD probands and 10 318 ASD probands) and 4262 controls. METHODS By curating NEMGs and cataloging publicly published DNVs in NEMGs, we compared the frequency of DNVs in cases and controls. We also applied a TADA-denovo model to highlight disease-associated NEMGs and characterized them based on gene intolerance, functional networks and expression patterns. RESULTS Compared with levels in 4262 controls, an excess of protein-truncating variants and deleterious missense variants in 1421 cataloged NEMGs from 41 376 patients (31 058 UDD and 10 318 ASD probands) was observed. Overall, 3.23% of de novo deleterious missense variants and 3.20% of de novo protein-truncating variants contributed to 1.1% and 0.39% of UDD-ASD cases, respectively. We prioritized 130 disease-associated NEMGs and showed distinct expression patterns in the developing human brain. Disease-associated NEMGs expression was enriched in both excitatory and inhibitory neuronal lineages from the developing human cortex. CONCLUSIONS Rare genetic alterations of disease-associated NEMGs may play a role in UDD-ASD development and lay the groundwork for a better understanding of the biology of UDD-ASD.
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Affiliation(s)
- T Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - J Pan
- Department of Birth Health and Genetics, The Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning 530022, China
| | - Y Zhu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - X Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - K Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - G Zhao
- 4National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008,China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - B Li
- 4National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008,China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Z Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - K Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- MOE Key Lab of Rare Pediatric Diseases & School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 410008, China
| | - J Li
- 4National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008,China
- Bioinformatics Center, Furong Laboratory & Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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Wan L, Yang G, Yan Z. Identification of a molecular network regulated by multiple ASD high risk genes. Hum Mol Genet 2024:ddae058. [PMID: 38588587 DOI: 10.1093/hmg/ddae058] [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: 12/11/2023] [Revised: 01/26/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Genetic sequencing has identified high-confidence ASD risk genes with loss-of-function mutations. How the haploinsufficiency of distinct ASD risk genes causes ASD remains to be elucidated. In this study, we examined the role of four top-ranking ASD risk genes, ADNP, KDM6B, CHD2, and MED13, in gene expression regulation. ChIP-seq analysis reveals that gene targets with the binding of these ASD risk genes at promoters are enriched in RNA processing and DNA repair. Many of these targets are found in ASD gene database (SFARI), and are involved in transcription regulation and chromatin remodeling. Common gene targets of these ASD risk genes include a network of high confidence ASD genes associated with gene expression regulation, such as CTNNB1 and SMARCA4. We further directly examined the transcriptional impact of the deficiency of these ASD risk genes. Our mRNA profiling with qPCR assays in cells with the knockdown of Adnp, Kdm6b, Chd2 or Med13 has revealed an intricate pattern of their cross-regulation, as well as their influence on the expression of other ASD genes. In addition, some synaptic genes, such as Snap25 and Nrxn1, are strongly regulated by deficiency of the four ASD risk genes, which could be through the direct binding at promoters or indirectly through the targets like Ctnnb1 or Smarca4. The identification of convergent and divergent gene targets that are regulated by multiple ASD risk genes will help to understand the molecular mechanisms underlying common and unique phenotypes associated with haploinsufficiency of ASD-associated genes.
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Affiliation(s)
- Lei Wan
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main Street, Buffalo, NY 14203, United States
| | - Guojun Yang
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main Street, Buffalo, NY 14203, United States
| | - Zhen Yan
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main Street, Buffalo, NY 14203, United States
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48
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Xu C, Bao S, Chen H, Jiang T, Zhang C. Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586363. [PMID: 38586002 PMCID: PMC10996483 DOI: 10.1101/2024.03.22.586363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods on various prediction tasks, including evolutionary sequence divergence on lineage-specific splicing and splicing-altering mutations in human populations and neurodevelopmental disorders, and demonstrated that DeltaSplice outperformed consistently. DeltaSplice predicted ~15% of splicing quantitative trait loci (sQTLs) in the human brain as causal splicing-altering variants. It also predicted splicing-altering de novo mutations outside the splice sites in a subset of patients affected by autism and other neurodevelopmental disorders, including 19 genes with recurrent splicing-altering mutations. Among the new candidate disease risk genes, MFN1 is involved in mitochondria fusion, which is frequently disrupted in autism patients. Our work expanded the capacity of in silico splicing models with potential applications in genetic diagnosis and the development of splicing-based precision medicine.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
- Present address: Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Suying Bao
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Present address: Regeneron Pharmaceuticals, Terrytown, NY 10591, USA
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
- Present address: Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tao Jiang
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
- Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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Garrido-Torres N, Marqués Rodríguez R, Alemany-Navarro M, Sánchez-García J, García-Cerro S, Ayuso MI, González-Meneses A, Martinez-Mir A, Ruiz-Veguilla M, Crespo-Facorro B. Exploring genetic testing requests, genetic alterations and clinical associations in a cohort of children with autism spectrum disorder. Eur Child Adolesc Psychiatry 2024:10.1007/s00787-024-02413-x. [PMID: 38587680 DOI: 10.1007/s00787-024-02413-x] [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: 11/18/2023] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Several studies show great heterogeneity in the type of genetic test requested and in the clinicopathological characteristics of patients with ASD. The following study aims, firstly, to explore the factors that might influence professionals' decisions about the appropriateness of requesting genetic testing for their patients with ASD and, secondly, to determine the prevalence of genetic alterations in a representative sample of children with a diagnosis of ASD. Methods: We studied the clinical factors associated with the request for genetic testing in a sample of 440 children with ASD and the clinical factors of present genetic alterations. Even though the main guidelines recommend genetic testing all children with an ASD diagnosis, only 56% of children with an ASD diagnosis were genetically tested. The prevalence of genetic alterations was 17.5%. These alterations were more often associated with intellectual disability and dysmorphic features. There are no objective data to explicitly justify the request for genetic testing, nor are there objective data to justify requesting one genetic study versus multiple studies. Remarkably, only 28% of males were genetically tested with the recommended tests (fragile X and CMA). Children with dysmorphic features and organic comorbidities were more likely to be genetic tested than those without. Previous diagnosis of ASD (family history of ASD) and attendance at specialist services were also associated with Genetically tested Autism Spectrum Disorder GTASD. Our findings emphasize the importance of establishing algorithms to facilitate targeted genetic consultation for individuals with ASD who are likely to benefit, considering clinical phenotypes, efficiency, ethics, and benefits.
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Affiliation(s)
- Nathalia Garrido-Torres
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
| | | | - María Alemany-Navarro
- Instituto de Biomedicina de Sevilla, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
| | - Javier Sánchez-García
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
- Department of Maternofetal Medicine, Genetics and Reproduction, Seville, Spain
- Spanish National Research Council (CSIC), Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Susana García-Cerro
- Instituto de Biomedicina de Sevilla, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
| | - María Irene Ayuso
- Instituto de Biomedicina de Sevilla, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
| | | | - Amalia Martinez-Mir
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
- Spanish National Research Council (CSIC), Seville, Spain
| | - Miguel Ruiz-Veguilla
- Instituto de Biomedicina de Sevilla, Seville, Spain
- University of Seville, Seville, Spain
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain
- Hospital Universitario Virgen del Rocío, Seville, Spain
| | - Benedicto Crespo-Facorro
- Instituto de Biomedicina de Sevilla, Seville, Spain.
- University of Seville, Seville, Spain.
- CIBERSAM, ISCIII (Spanish Network for Research in Mental Health), Seville, Spain.
- Hospital Universitario Virgen del Rocío, Seville, Spain.
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Wynn J, Karlsen A, Huber B, Levine A, Salem A, White LC, Luby M, Bezborodko E, Xiao S, Chung WK, Klitzman RL, Appelbaum PS. Impact of a Genetic Diagnosis for a Child's Autism on Parental Perceptions. J Autism Dev Disord 2024:10.1007/s10803-024-06273-x. [PMID: 38578549 DOI: 10.1007/s10803-024-06273-x] [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] [Accepted: 01/28/2024] [Indexed: 04/06/2024]
Abstract
Genetic testing is recommended as part of an autism assessment, and most parents support genetic testing for their minor children. However, the impact on parents of receiving a monogenetic/ copy number variant diagnosis for autism in their child is not well understood. To explore this, we surveyed and interviewed parents of children in the SPARK study, a study of autism that includes genetic testing. Surveys were administered one month before and one and 12 months after parents received their child's genetic result. Interviews were conducted approximately one month after results disclosure. A genetic diagnosis (GD) for their child appeared to reduce parents' sense of self-blame and feelings of guilt, and this impact was relatively stable. The data also indicate a modest impact on parents' actions related to the condition, perceptions of themselves, and some aspects of life planning for their child, as measured by quantitative instruments at one month and 12 months after receipt of results. Other measures of parental identity and expectations for their child, in contrast, showed little change following receipt of genetic findings. Overall, parents who were told that no GD was identified showed minimal changes in their responses over time. These results suggest a discernable but relatively limited impact of genetic test results on parents of children with autism. These results should be reassuring to clinicians caring for children with autism and are consistent with studies in other areas of medicine that have suggested that genetic results tend to have fewer effects-negative or positive-than were anticipated.
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Affiliation(s)
- Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
| | - Anna Karlsen
- Columbia University Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Benjamin Huber
- Department of Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alina Levine
- Department of Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Amanie Salem
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | - Ekaterina Bezborodko
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Simons Foundation, New York, NY, USA
- Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert L Klitzman
- Department of Psychiatry and Masters of Bioethics Program, and New York State Psychiatric Institute, Columbia University, New York, NY, USA
| | - Paul S Appelbaum
- Department of Psychiatry, and New York State Psychiatric Institute, Columbia University Irving Medical Center, New York, NY, USA
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