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Denisova K, Wolpert DM. Sensorimotor variability distinguishes early features of cognition in toddlers with autism. iScience 2024; 27:110685. [PMID: 39252975 PMCID: PMC11381898 DOI: 10.1016/j.isci.2024.110685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/03/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024] Open
Abstract
The potential role of early sensorimotor features to atypical human cognition in autistic children has received surprisingly little attention given that appropriate movements are a crucial element that connects us to other people. We examined quantitative and observation-based movements in over 1,000 toddlers diagnosed with autism spectrum disorder (ASD) with different levels of cognitive abilities (intelligence quotient, IQ). Relative to higher-IQ ASD toddlers, those with lower-IQ had significantly altered sensorimotor features. Remarkably, we found that higher IQ in autistic toddlers confers resilience to atypical movement, as sensorimotor features in higher-IQ ASD children were indistinguishable from those of typically developing healthy control toddlers. We suggest that the altered movement patterns may affect key autistic behaviors in those with lower intelligence by affecting sensorimotor learning mechanisms. Atypical sensorimotor functioning is a key feature in lower-IQ early childhood autism. These findings have implications for the development of individualized interventions for subtypes of autism.
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Affiliation(s)
- Kristina Denisova
- Division of Math and Natural Sciences, Department of Psychology, Autism Origins Lab, City University of New York, Queens College and Graduate Center, New York, NY 10032, USA
| | - Daniel M Wolpert
- Zuckerman Mind Brain Behavior Institute & Department of Neuroscience, Columbia University, New York, NY 10027, USA
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2
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Katsanevaki D, Till SM, Buller-Peralta I, Nawaz MS, Louros SR, Kapgal V, Tiwari S, Walsh D, Anstey NJ, Petrović NG, Cormack A, Salazar-Sanchez V, Harris A, Farnworth-Rowson W, Sutherland A, Watson TC, Dimitrov S, Jackson AD, Arkell D, Biswal S, Dissanayake KN, Mizen LAM, Perentos N, Jones MW, Cousin MA, Booker SA, Osterweil EK, Chattarji S, Wyllie DJA, Gonzalez-Sulser A, Hardt O, Wood ER, Kind PC. Key roles of C2/GAP domains in SYNGAP1-related pathophysiology. Cell Rep 2024; 43:114733. [PMID: 39269903 DOI: 10.1016/j.celrep.2024.114733] [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: 01/18/2023] [Revised: 07/30/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
Mutations in SYNGAP1 are a common genetic cause of intellectual disability (ID) and a risk factor for autism. SYNGAP1 encodes a synaptic GTPase-activating protein (GAP) that has both signaling and scaffolding roles. Most pathogenic variants of SYNGAP1 are predicted to result in haploinsufficiency. However, some affected individuals carry missense mutations in its calcium/lipid binding (C2) and GAP domains, suggesting that many clinical features result from loss of functions carried out by these domains. To test this hypothesis, we targeted the exons encoding the C2 and GAP domains of SYNGAP. Rats heterozygous for this deletion exhibit reduced exploration and fear extinction, altered social investigation, and spontaneous seizures-key phenotypes shared with Syngap heterozygous null rats. Together, these findings indicate that the reduction of SYNGAP C2/GAP domain function is a main feature of SYNGAP haploinsufficiency. This rat model provides an important system for the study of ID, autism, and epilepsy.
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Affiliation(s)
- Danai Katsanevaki
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Sally M Till
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Ingrid Buller-Peralta
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Mohammad Sarfaraz Nawaz
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Susana R Louros
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Vijayakumar Kapgal
- Centre for Brain Development and Repair, Instem, Bangalore 560065, India; The University of Transdisciplinary Health Sciences and Technology, Bangalore 560065, India
| | - Shashank Tiwari
- Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Darren Walsh
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Natasha J Anstey
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Nina G Petrović
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Alison Cormack
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Vanesa Salazar-Sanchez
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Anjanette Harris
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - William Farnworth-Rowson
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Andrew Sutherland
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Thomas C Watson
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Siyan Dimitrov
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Adam D Jackson
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Daisy Arkell
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | | | - Kosala N Dissanayake
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Lindsay A M Mizen
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Nikolas Perentos
- Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Matt W Jones
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, UK
| | - Michael A Cousin
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Sam A Booker
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Emily K Osterweil
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Sumantra Chattarji
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - David J A Wyllie
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Alfredo Gonzalez-Sulser
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK
| | - Oliver Hardt
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India; Department of Psychology, McGill University, Montreal, QC H3A 1G1, Canada
| | - Emma R Wood
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India
| | - Peter C Kind
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, EH8 9XD Edinburgh, UK; Patrick Wild Centre, University of Edinburgh, EH8 9XD Edinburgh, UK; Centre for Brain Development and Repair, Instem, Bangalore 560065, India.
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3
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Ferraguto C, Piquemal-Lagoueillat M, Lemaire V, Moreau MM, Trazzi S, Uguagliati B, Ciani E, Bertrand SS, Louette E, Bontempi B, Pietropaolo S. Therapeutic efficacy of the BKCa channel opener chlorzoxazone in a mouse model of Fragile X syndrome. Neuropsychopharmacology 2024:10.1038/s41386-024-01956-6. [PMID: 39223257 DOI: 10.1038/s41386-024-01956-6] [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: 03/14/2024] [Revised: 06/30/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Fragile X syndrome (FXS) is an X-linked neurodevelopmental disorder characterized by several behavioral abnormalities, including hyperactivity, anxiety, sensory hyper-responsiveness, and autistic-like symptoms such as social deficits. Despite considerable efforts, effective pharmacological treatments are still lacking, prompting the need for exploring the therapeutic value of existing drugs beyond their original approved use. One such repurposed drug is chlorzoxazone which is classified as a large-conductance calcium-dependent potassium (BKCa) channel opener. Reduced BKCa channel functionality has been reported in FXS patients, suggesting that molecules activating these channels could serve as promising treatments for this syndrome. Here, we sought to characterize the therapeutic potential of chlorzoxazone using the Fmr1-KO mouse model of FXS which recapitulates the main phenotypes of FXS, including BKCa channel alterations. Chlorzoxazone, administered either acutely or chronically, rescued hyperactivity and acoustic hyper-responsiveness as well as impaired social interactions exhibited by Fmr1-KO mice. Chlorzoxazone was more efficacious in alleviating these phenotypes than gaboxadol and metformin, two repurposed treatments for FXS that do not target BKCa channels. Systemic administration of chlorzoxazone modulated the neuronal activity-dependent gene c-fos in selected brain areas of Fmr1-KO mice, corrected aberrant hippocampal dendritic spines, and was able to rescue impaired BKCa currents recorded from hippocampal and cortical neurons of these mutants. Collectively, these findings provide further preclinical support for BKCa channels as a valuable therapeutic target for treating FXS and encourage the repurposing of chlorzoxazone for clinical applications in FXS and other related neurodevelopmental diseases.
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Affiliation(s)
| | | | - Valerie Lemaire
- Univ. Bordeaux, CNRS, EPHE, INCIA, UMR 5287, Bordeaux, France
| | - Maïté M Moreau
- Univ. Bordeaux, INSERM, Neurocentre Magendie, U1215, Bordeaux, France
| | - Stefania Trazzi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Beatrice Uguagliati
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Elisabetta Ciani
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | | | | | - Bruno Bontempi
- Univ. Bordeaux, CNRS, EPHE, INCIA, UMR 5287, Bordeaux, France
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4
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Garcia MF, Retallick-Townsley K, Pruitt A, Davidson E, Dai Y, Fitzpatrick SE, Sen A, Cohen S, Livoti O, Khan S, Dossou G, Cheung J, Deans PJM, Wang Z, Huckins L, Hoffman E, Brennand K. Dynamic convergence of autism disorder risk genes across neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609190. [PMID: 39229156 PMCID: PMC11370590 DOI: 10.1101/2024.08.23.609190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Over a hundred risk genes underlie risk for autism spectrum disorder (ASD) but the extent to which they converge on shared downstream targets to increase ASD risk is unknown. To test the hypothesis that cellular context impacts the nature of convergence, here we apply a pooled CRISPR approach to target 29 ASD loss-of-function genes in human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells, glutamatergic neurons, and GABAergic neurons. Two distinct approaches (gene-level and network-level analyses) demonstrate that convergence is greatest in mature glutamatergic neurons. Convergent effects are dynamic, varying in strength, composition, and biological role between cell types, increasing with functional similarity of the ASD genes examined, and driven by cell-type-specific gene co-expression patterns. Stratification of ASD genes yield targeted drug predictions capable of reversing gene-specific convergent signatures in human cells and ASD-related behaviors in zebrafish. Altogether, convergent networks downstream of ASD risk genes represent novel points of individualized therapeutic intervention.
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Affiliation(s)
- Meilin Fernandez Garcia
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Kayla Retallick-Townsley
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - April Pruitt
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Elizabeth Davidson
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Yi Dai
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Sarah E Fitzpatrick
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Annabel Sen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Sophie Cohen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Olivia Livoti
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Suha Khan
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Grace Dossou
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Jen Cheung
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - P J Michael Deans
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Zuoheng Wang
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Laura Huckins
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ellen Hoffman
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Kristen Brennand
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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5
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Wang H, Chang TS, Dombroski BA, Cheng PL, Patil V, Valiente-Banuet L, Farrell K, Mclean C, Molina-Porcel L, Rajput A, De Deyn PP, Le Bastard N, Gearing M, Kaat LD, Van Swieten JC, Dopper E, Ghetti BF, Newell KL, Troakes C, de Yébenes JG, Rábano-Gutierrez A, Meller T, Oertel WH, Respondek G, Stamelou M, Arzberger T, Roeber S, Müller U, Hopfner F, Pastor P, Brice A, Durr A, Le Ber I, Beach TG, Serrano GE, Hazrati LN, Litvan I, Rademakers R, Ross OA, Galasko D, Boxer AL, Miller BL, Seeley WW, Van Deerlin VM, Lee EB, White CL, Morris H, de Silva R, Crary JF, Goate AM, Friedman JS, Leung YY, Coppola G, Naj AC, Wang LS, Dalgard C, Dickson DW, Höglinger GU, Schellenberg GD, Geschwind DH, Lee WP. Whole-genome sequencing analysis reveals new susceptibility loci and structural variants associated with progressive supranuclear palsy. Mol Neurodegener 2024; 19:61. [PMID: 39152475 PMCID: PMC11330058 DOI: 10.1186/s13024-024-00747-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Progressive supranuclear palsy (PSP) is a rare neurodegenerative disease characterized by the accumulation of aggregated tau proteins in astrocytes, neurons, and oligodendrocytes. Previous genome-wide association studies for PSP were based on genotype array, therefore, were inadequate for the analysis of rare variants as well as larger mutations, such as small insertions/deletions (indels) and structural variants (SVs). METHOD In this study, we performed whole genome sequencing (WGS) and conducted association analysis for single nucleotide variants (SNVs), indels, and SVs, in a cohort of 1,718 cases and 2,944 controls of European ancestry. Of the 1,718 PSP individuals, 1,441 were autopsy-confirmed and 277 were clinically diagnosed. RESULTS Our analysis of common SNVs and indels confirmed known genetic loci at MAPT, MOBP, STX6, SLCO1A2, DUSP10, and SP1, and further uncovered novel signals in APOE, FCHO1/MAP1S, KIF13A, TRIM24, TNXB, and ELOVL1. Notably, in contrast to Alzheimer's disease (AD), we observed the APOE ε2 allele to be the risk allele in PSP. Analysis of rare SNVs and indels identified significant association in ZNF592 and further gene network analysis identified a module of neuronal genes dysregulated in PSP. Moreover, seven common SVs associated with PSP were observed in the H1/H2 haplotype region (17q21.31) and other loci, including IGH, PCMT1, CYP2A13, and SMCP. In the H1/H2 haplotype region, there is a burden of rare deletions and duplications (P = 6.73 × 10-3) in PSP. CONCLUSIONS Through WGS, we significantly enhanced our understanding of the genetic basis of PSP, providing new targets for exploring disease mechanisms and therapeutic interventions.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy S Chang
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vishakha Patil
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Leopoldo Valiente-Banuet
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kurt Farrell
- Department of Pathology, Department of Artificial Intelligence & Human Health, Nash Family, Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain, Institute, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catriona Mclean
- Victorian Brain Bank, The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Laura Molina-Porcel
- Alzheimer's Disease and Other Cognitive Disorders Unit. Neurology Service, Hospital Clínic, Fundació Recerca Clínic Barcelona (FRCB). Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Neurological Tissue Bank of the Biobanc-Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Alex Rajput
- Movement Disorders Program, Division of Neurology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Peter Paul De Deyn
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, University of Antwerp, Wilrijk (Antwerp), Belgium
- Department of Neurology, University Medical Center Groningen, NL-9713 AV, Groningen, Netherlands
| | | | - Marla Gearing
- Department of Pathology and Laboratory Medicine and Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Laura Donker Kaat
- Netherlands Brain Bank and Erasmus University, Rotterdam, Netherlands
| | | | - Elise Dopper
- Netherlands Brain Bank and Erasmus University, Rotterdam, Netherlands
| | - Bernardino F Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | | | - Alberto Rábano-Gutierrez
- Fundación CIEN (Centro de Investigación de Enfermedades Neurológicas) - Centro Alzheimer Fundación Reina Sofía, Madrid, Spain
| | - Tina Meller
- Department of Neurology, Philipps-Universität, Marburg, Germany
| | | | - Gesine Respondek
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Maria Stamelou
- Parkinson's Disease and Movement Disorders Department, HYGEIA Hospital, Athens, Greece
- European University of Cyprus, Nicosia, Cyprus
| | - Thomas Arzberger
- Department of Psychiatry and Psychotherapy, University Hospital Munich, Ludwig-Maximilians-University Munich, Munich, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sigrun Roeber
- German Brain Bank, Neurobiobank Munich, Munich, Germany
| | - Ulrich Müller
- German Brain Bank, Neurobiobank Munich, Munich, Germany
| | - Franziska Hopfner
- Department of Neurology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) München; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Pau Pastor
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias I Pujol, Badalona, Barcelona, Spain
- Neurosciences, The Germans Trias I Pujol Research Institute (IGTP) Badalona, Badalona, Spain
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Isabelle Le Ber
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | | | - Irene Litvan
- Department of Neuroscience, University of California, San Diego, CA, USA
| | - Rosa Rademakers
- VIB Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA
| | - Douglas Galasko
- Department of Neuroscience, University of California, San Diego, CA, USA
| | - Adam L Boxer
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Bruce L Miller
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Willian W Seeley
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Vivanna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charles L White
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huw Morris
- Departmento of Clinical and Movement Neuroscience, University College of London, London, UK
| | - Rohan de Silva
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - John F Crary
- Department of Pathology, Department of Artificial Intelligence & Human Health, Nash Family, Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain, Institute, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giovanni Coppola
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Clifton Dalgard
- Department of Anatomy Physiology and Genetics, the American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL, USA.
| | - Günter U Höglinger
- Department of Neurology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) München; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Daniel H Geschwind
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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6
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Yim KM, Baumgartner M, Krenzer M, Rosales Larios MF, Hill-Terán G, Nottoli T, Muhle RA, Noonan JP. Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.608000. [PMID: 39185167 PMCID: PMC11343218 DOI: 10.1101/2024.08.14.608000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Disruptive variants in the chromodomain helicase CHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited. We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type and Chd8 +/- mouse cortex, respectively. Chd8 and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated in Chd8 +/- embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated in Chd8 +/- postnatal day (P) 25 deep- and upper-layer excitatory cortical neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation in Chd8 +/- developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage.
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Affiliation(s)
- Kristina M. Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Martina Krenzer
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Mount Sinai School of Medicine, Brookdale Department of Geriatrics and Palliative Medicine, New York, NY 10029, USA
| | - María F. Rosales Larios
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Social Studies of Science and Technology, Department of Evolutionary Biology, School of Sciences, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Guillermina Hill-Terán
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Higher Institute of Biological Research (INSIBIO, CONICET-UNT), Institute of Biology, National University of Tucumán, T4000 San Miguel de Tucumán, Argentina
| | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Rebecca A. Muhle
- Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA
- Present address: New York State Psychiatric Institute and Columbia University Department of Psychiatry, New York, NY 10032, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
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7
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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] [MESH Headings] [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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8
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Wang L, Wang C, Moriano JA, Chen S, Zuo G, Cebrián-Silla A, Zhang S, Mukhtar T, Wang S, Song M, de Oliveira LG, Bi Q, Augustin JJ, Ge X, Paredes MF, Huang EJ, Alvarez-Buylla A, Duan X, Li J, Kriegstein AR. Molecular and cellular dynamics of the developing human neocortex at single-cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575956. [PMID: 39131371 PMCID: PMC11312442 DOI: 10.1101/2024.01.16.575956] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The development of the human neocortex is a highly dynamic process and involves complex cellular trajectories controlled by cell-type-specific gene regulation1. Here, we collected paired single-nucleus chromatin accessibility and transcriptome data from 38 human neocortical samples encompassing both the prefrontal cortex and primary visual cortex. These samples span five main developmental stages, ranging from the first trimester to adolescence. In parallel, we performed spatial transcriptomic analysis on a subset of the samples to illustrate spatial organization and intercellular communication. This atlas enables us to catalog cell type-, age-, and area-specific gene regulatory networks underlying neural differentiation. Moreover, combining single-cell profiling, progenitor purification, and lineage-tracing experiments, we have untangled the complex lineage relationships among progenitor subtypes during the transition from neurogenesis to gliogenesis in the human neocortex. We identified a tripotential intermediate progenitor subtype, termed Tri-IPC, responsible for the local production of GABAergic neurons, oligodendrocyte precursor cells, and astrocytes. Remarkably, most glioblastoma cells resemble Tri-IPCs at the transcriptomic level, suggesting that cancer cells hijack developmental processes to enhance growth and heterogeneity. Furthermore, by integrating our atlas data with large-scale GWAS data, we created a disease-risk map highlighting enriched ASD risk in second-trimester intratelencephalic projection neurons. Our study sheds light on the gene regulatory landscape and cellular dynamics of the developing human neocortex.
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Affiliation(s)
- Li Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Cheng Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Juan A Moriano
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
- University of Barcelona Institute of Complex Systems; Barcelona, 08007, Spain
| | - Songcang Chen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Guolong Zuo
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Arantxa Cebrián-Silla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California San Francisco; San Francisco, CA 94143, USA
| | - Shaobo Zhang
- Department of Ophthalmology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Tanzila Mukhtar
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Shaohui Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Mengyi Song
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Lilian Gomes de Oliveira
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Neuro-immune Interactions Laboratory, Institute of Biomedical Sciences, Department of Immunology, University of São Paulo; São Paulo, SP 05508-220, Brazil
| | - Qiuli Bi
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Jonathan J Augustin
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Xinxin Ge
- Department of Physiology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mercedes F Paredes
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Eric J Huang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Pathology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Arturo Alvarez-Buylla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California San Francisco; San Francisco, CA 94143, USA
| | - Xin Duan
- Department of Ophthalmology, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Physiology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jingjing Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
| | - Arnold R Kriegstein
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco; San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco; San Francisco, CA 94143, USA
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9
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Starr AL, Fraser HB. A general principle governing neuronal evolution reveals a human-accelerated neuron type potentially underlying the high prevalence of autism in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606407. [PMID: 39131279 PMCID: PMC11312593 DOI: 10.1101/2024.08.02.606407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106 neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons-layer 2/3 intratelencephalic excitatory neurons-has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In sum, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.
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Affiliation(s)
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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10
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Hong Y, Hu J, Zhang S, Liu J, Yan F, Yang H, Hu H. Integrative analysis identifies region- and sex-specific gene networks and Mef2c as a mediator of anxiety-like behavior. Cell Rep 2024; 43:114455. [PMID: 38990717 DOI: 10.1016/j.celrep.2024.114455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/20/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The molecular mechanisms underlying multi-brain region origins and sexual dimorphism of anxiety remain unclear. Here, we leverage large-scale transcriptomics from seven brain regions in mouse models of anxiety and extensive experiments to dissect brain-region- and sex-specific gene networks. We identify 4,840 genes with sex-specific expression alterations across seven brain regions, organized into ten network modules with sex-biased expression patterns. Modular analysis prioritizes 86 sex-specific mediators of anxiety susceptibility, including myocyte-specific enhancer factor 2c (Mef2c) in the CA3 region of male mice. Mef2c expression is decreased in the pyramidal neurons (PyNs) of susceptible male mice. Up-regulating Mef2c in CA3 PyNs significantly alleviates anxiety-like behavior, whereas down-regulating Mef2c induces anxiety-like behavior in male mice. The anxiolytic effect of Mef2c up-regulation is associated with enhanced neuronal excitability and synaptic transmission. In summary, this study uncovers brain-region- and sex-specific networks and identifies Mef2c in CA3 PyNs as a critical mediator of anxiety in male mice.
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Affiliation(s)
- Yizhou Hong
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Jiameng Hu
- School of Life Science and Technology, Chongqing Innovation Institute of China Pharmaceutical University, China Pharmaceutical University, Nanjing, China
| | - Shiya Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; College of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jiaxin Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; College of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangrong Yan
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hua Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
| | - Haiyang Hu
- School of Life Science and Technology, Chongqing Innovation Institute of China Pharmaceutical University, China Pharmaceutical University, Nanjing, China; Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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11
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Russ JB, Stone AC, Maney K, Morris L, Wright CF, Hurst JH, Cohen JL. Pathogenic variants associated with speech/cognitive delay and seizures affect genes with expression biases in excitatory neurons and microglia in developing human cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601597. [PMID: 39005386 PMCID: PMC11245013 DOI: 10.1101/2024.07.01.601597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background & Objective Congenital brain malformations and neurodevelopmental disorders (NDDs) are common pediatric neurological disorders and result in chronic disability. With the expansion of genetic testing, new etiologies for NDDs are continually uncovered, with as many as one third attributable to single-gene pathogenic variants. While our ability to identify pathogenic variants has continually improved, we have little understanding of the underlying cellular pathophysiology in the nervous system that results from these variants. We therefore integrated phenotypic information from subjects with monogenic diagnoses with two large, single-nucleus RNA-sequencing (snRNAseq) datasets from human cortex across developmental stages in order to investigate cell-specific biases in gene expression associated with distinct neurodevelopmental phenotypes. Methods Phenotypic data was gathered from 1) a single-institution cohort of 84 neonates with pathogenic single-gene variants referred to Duke Pediatric Genetics, and 2) a cohort of 4,238 patients with neurodevelopmental disorders and pathogenic single-gene variants enrolled in the Deciphering Developmental Disorders (DDD) study. Pathogenic variants were grouped into genesets by neurodevelopmental phenotype and geneset expression across cortical cell subtypes was compared within snRNAseq datasets from 86 human cortex samples spanning the 2nd trimester of gestation to adulthood. Results We find that pathogenic variants associated with speech/cognitive delay or seizures involve genes that are more highly expressed in cortical excitatory neurons than variants in genes not associated with these phenotypes (Speech/cognitive: p=2.25×10-7; Seizures: p=7.97×10-12). A separate set of primarily rare variants associated with speech/cognitive delay or seizures, distinct from those with excitatory neuron expression biases, demonstrated expression biases in microglia. We also found that variants associated with speech/cognitive delay and an excitatory neuron expression bias could be further parsed by the presence or absence of comorbid seizures. Variants associated with speech/cognitive delay without seizures tended to involve calcium regulatory pathways and showed greater expression in extratelencephalic neurons, while those associated with speech/cognitive delay with seizures tended to involve synaptic regulatory machinery and an intratelencephalic neuron expression bias (ANOVA by geneset p<2×10-16). Conclusions By combining extensive phenotype datasets from subjects with neurodevelopmental disorders with massive human cortical snRNAseq datasets across developmental stages, we identified cell-specific expression biases for genes in which pathogenic variants are associated with speech/cognitive delay and seizures. The involvement of genes with enriched expression in excitatory neurons or microglia highlights the unique role both cell types play in proper sculpting of the developing brain. Moreover, this information begins to shed light on distinct cortical cell types that are more likely to be impacted by pathogenic variants and that may mediate the symptomatology of resulting neurodevelopmental disorders.
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Affiliation(s)
- Jeffrey B Russ
- Department of Pediatrics, Division of Neurology, Duke University, USA
| | - Alexa C Stone
- Department of Pediatrics, Pediatric Neurology Residency Program, Duke University, USA
| | - Kayli Maney
- Department of Pediatrics, Pediatric Neurology Residency Program, Duke University, USA
| | - Lauren Morris
- Department of Pediatrics, Pediatric Neurology Residency Program, Duke University, USA
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter, UK
| | - Jillian H Hurst
- Department of Pediatrics, Children's Health & Discovery Initiative, Duke University, USA
| | - Jennifer L Cohen
- Department of Pediatrics, Division of Medical Genetics, Duke University, USA
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12
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Umair M, Alharbi M, Aloyouni E, Al Abdulrahman A, Aldrees M, Al Tuwaijri A, Bilal M, Alfadhel M. Mutated neuron navigator 3 as a candidate gene for a rare neurodevelopmental disorder. Mol Genet Genomic Med 2024; 12:e2473. [PMID: 39038237 PMCID: PMC11262617 DOI: 10.1002/mgg3.2473] [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: 03/02/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 07/24/2024] Open
Abstract
BACKGROUND Neuron navigator 3 (NAV3) is characterized as one of the neuron navigator family (NAV1, NAV2, NAV3) proteins predominantly expressed in the nervous system. The NAV3-encoded protein comprises a conserved AAA and coiled-coil domains characteristic of ATPases, which are associated with different cellular activities. METHODS We describe a Saudi proband presenting a complex recessive neurodevelopmental disorder (NDD). Whole exome sequencing (WES) followed by Sanger sequencing, 3D protein modeling and RT-qPCR was performed. RESULTS WES revealed a bi-allelic frameshift variant (c.2604_2605delAG; p.Val870SerfsTer12) in exon 12 of the NAV3 gene. Furthermore, RT-qPCR revealed a significant decrease in the NAV3 mRNA expression in the patient sample, and 3D protein modeling revealed disruption of the overall secondary structure. CONCLUSION For the time, we associate a bi-allelic variant in the NAV3 gene causing NDD in humans.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC)King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS), Ministry of National Guard Health Affairs (MNGH)RiyadhSaudi Arabia
| | - Meshael Alharbi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC)King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS), Ministry of National Guard Health Affairs (MNGH)RiyadhSaudi Arabia
| | - Essra Aloyouni
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC)King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS), Ministry of National Guard Health Affairs (MNGH)RiyadhSaudi Arabia
| | - Abdulkareem Al Abdulrahman
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC)King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS), Ministry of National Guard Health Affairs (MNGH)RiyadhSaudi Arabia
| | - Mohammed Aldrees
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC)King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS), Ministry of National Guard Health Affairs (MNGH)RiyadhSaudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC)King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS), Ministry of National Guard Health Affairs (MNGH)RiyadhSaudi Arabia
- Clinical Laboratory Sciences DepartmentCollege of Applied Medical Sciences, KSAU‐HSRiyadhSaudi Arabia
| | - Muhammad Bilal
- Department of Pathology and Laboratory MedicineAga Khan UniversityKarachiPakistan
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC)King Saud Bin Abdulaziz University for Health Sciences (KSAU‐HS), Ministry of National Guard Health Affairs (MNGH)RiyadhSaudi Arabia
- Genetics and Precision Medicine DepartmentKing Abdullah Specialized Children Hospital (KASCH), MNGHARiyadhSaudi Arabia
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13
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Fazel Darbandi S, An JY, Lim K, Page NF, Liang L, Young DM, Ypsilanti AR, State MW, Nord AS, Sanders SJ, Rubenstein JLR. Five autism-associated transcriptional regulators target shared loci proximal to brain-expressed genes. Cell Rep 2024; 43:114329. [PMID: 38850535 PMCID: PMC11235582 DOI: 10.1016/j.celrep.2024.114329] [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: 05/29/2023] [Revised: 09/15/2023] [Accepted: 05/22/2024] [Indexed: 06/10/2024] Open
Abstract
Many autism spectrum disorder (ASD)-associated genes act as transcriptional regulators (TRs). Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify the regulatory targets of ARID1B, BCL11A, FOXP1, TBR1, and TCF7L2, ASD-associated TRs in the developing human and mouse cortex. These TRs shared substantial overlap in the binding sites, especially within open chromatin. The overlap within a promoter region, 1-2,000 bp upstream of the transcription start site, was highly predictive of brain-expressed genes. This signature was observed in 96 out of 102 ASD-associated genes. In vitro CRISPRi against ARID1B and TBR1 delineated downstream convergent biology in mouse cortical cultures. After 8 days, NeuN+ and CALB+ cells were decreased, GFAP+ cells were increased, and transcriptomic signatures correlated with the postmortem brain samples from individuals with ASD. We suggest that functional convergence across five ASD-associated TRs leads to shared neurodevelopmental outcomes of haploinsufficient disruption.
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Affiliation(s)
- Siavash Fazel Darbandi
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, South Korea; BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, South Korea
| | - Kenneth Lim
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicholas F Page
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lindsay Liang
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David M Young
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Athena R Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - Stephan J Sanders
- Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA; Institute for Developmental and Regenerative Medicine, Old Road Campus, Roosevelt Dr., Headington, Oxford OX3 7TY, UK.
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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14
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Mato-Blanco X, Kim SK, Jourdon A, Ma S, Tebbenkamp AT, Liu F, Duque A, Vaccarino FM, Sestan N, Colantuoni C, Rakic P, Santpere G, Micali N. Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598925. [PMID: 38915580 PMCID: PMC11195173 DOI: 10.1101/2024.06.14.598925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.
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Affiliation(s)
- Xoel Mato-Blanco
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Suel-Kee Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alexandre Jourdon
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Fuchen Liu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alvaro Duque
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Flora M. Vaccarino
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Departments of Psychiatry, Genetics and Comparative Medicine, Wu Tsai Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Carlo Colantuoni
- Depts. of Neurology, Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pasko Rakic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriel Santpere
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Nicola Micali
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
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15
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Regulation of histone proteins affects gene expression through multiple mechanisms including exchange with histone variants. However, widely expressed variants of H2B remain elusive. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE, and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation, neuronal function, and memory. This work further identifies the first widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
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Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine C. Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Anna J. Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Shreya D. Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Camille N. Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine T. Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marc V. Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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16
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Denisova K. Neurobiology of cognitive abilities in early childhood autism. JCPP ADVANCES 2024; 4:e12214. [PMID: 38827984 PMCID: PMC11143961 DOI: 10.1002/jcv2.12214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/12/2023] [Indexed: 06/05/2024] Open
Abstract
This perspective considers complexities in the relationship between impaired cognitive abilities and autism from a maturational, developmental perspective, and aims to serve as a helpful guide for the complex and growing investigation of cognitive abilities and Autism Spectrum Disorder (ASD). Low Intelligence Quotient (IQ) and ASD are frequently co-occurring. About 37% of 8-year old children and 48% of 4-year old children diagnosed with ASD also have Intellectual Disability, with IQ below 70. And, low IQ in early infancy, including below 1 year of age, carries a 40% greater chance of receiving ASD diagnosis in early childhood. We consider the evidence that may explain this co-occurrence, including the possibility that high IQ may "rescue" the social communication issues, as well as the possible role of critical periods during growth and development. We consider how early low IQ may subsume a part of a subgroup of individuals with ASD, in particular, those diagnosed with autism in very early childhood, and we provide neurobiological evidence in support of this subtype. Moreover, we distinguish the concept of early low IQ from the delay in speech onset in preschool and school-aged children, based on (i) age and (ii) impairments in both verbal and non-verbal domains. The etiology of these early-diagnosed, early low IQ ASD cases is different from later-diagnosed, average or higher-IQ cases, and from children with speech delay onset. Given recent interest in formulating new subtypes of autism, rather than continuing to conceive of ASD as a spectrum, as well as new subtypes that vary in the degree of severity along the spectrum, we identify gaps in knowledge and directions for future work in this complex and growing area.
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Affiliation(s)
- Kristina Denisova
- Division of Math and Natural SciencesDepartment of PsychologyAutism Origins LabCity University of New YorkQueens College and Graduate CenterQueensNew YorkUSA
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17
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Bicks LK, Geschwind DH. Functional neurogenomics in autism spectrum disorders: A decade of progress. Curr Opin Neurobiol 2024; 86:102858. [PMID: 38547564 DOI: 10.1016/j.conb.2024.102858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 06/11/2024]
Abstract
Advances in autism spectrum disorder (ASD) genetics have identified many genetic causes, reflecting remarkable progress while at the same time identifying challenges such as heterogeneity and pleiotropy, which complicate attempts to connect genetic risk to mechanisms. High-throughput functional genomic approaches have yielded progress by defining a molecular pathology in the brain of individuals with ASD and in identifying convergent biological pathways through which risk genes are predicted to act. These studies indicate that ASD genetic risk converges in early brain development, primarily during the period of cortical neurogenesis. Over development, genetic perturbations in turn lead to broad neuronal signaling dysregulation, most prominent in glutamatergic cortical-cortical projecting neurons and somatostatin positive interneurons, which is accompanied by glial dyshomeostasis throughout the cerebral cortex. Connecting these developmental perturbations to disrupted neuronal and glial function in the postnatal brain is an important direction in current research. Coupling functional genomic approaches with advances in induced pluripotent stem cell-derived neural organoid development provides a promising avenue for connecting brain pathology to developmental mechanisms.
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Affiliation(s)
- Lucy K Bicks
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA. https://twitter.com/Bickslucy
| | - D H Geschwind
- Program in Neurobehavioral Genetics, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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18
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Badhe S, Nivins S, Kulkarni P, Jose A, Manek D, Badhe S, Sane H, Gokulchandran N, Badhe P, Sharma A. Abnormal Development of the Corpus Callosum in Autism Spectrum Disorder: An MRI Study. Top Magn Reson Imaging 2024; 33:e0312. [PMID: 38836588 DOI: 10.1097/rmr.0000000000000312] [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: 12/02/2023] [Accepted: 03/20/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Altered size in the corpus callosum (CC) has been reported in individuals with autism spectrum disorder (ASD), but few studies have investigated younger children. Moreover, knowledge about the age-related changes in CC size in individuals with ASD is limited. OBJECTIVES Our objective was to investigate the age-related size of the CC and compare them with age-matched healthy controls between the ages of 2 and 18 years. METHODS Structural-weighted images were acquired in 97 male patients diagnosed with ASD; published data were used for the control group. The CC was segmented into 7 distinct subregions (rostrum, genu, rostral body, anterior midbody, posterior midbody, isthmus, and splenium) as per Witelson's technique using ITK-SNAP software. We calculated both the total length and volume of the CC as well as the length and height of its 7 subregions. The length of the CC measures was studied as both continuous and categorical forms. For the continuous form, Pearson's correlation was used, while categorical forms were based on age ranges reflecting brain expansion during early postnatal years. Differences in CC measures between adjacent age groups in individuals with ASD were assessed using a Student t-test. Mean and standard deviation scores were compared between ASD and control groups using the Welch t-test. RESULTS Age showed a moderate positive association with the total length of the CC (r = 0.43; Padj = 0.003) among individuals with ASD. Among the subregions, a positive association was observed only in the anterior midbody of the CC (r = 0.41; Padj = 0.01). No association was found between the age and the height of individual subregions or with the total volume of the CC. In comparison with healthy controls, individuals with ASD exhibited shorter lengths and heights of the genu and splenium of the CC across wide age ranges. CONCLUSION Overall, our results highlight a distinct abnormal developmental trajectory of CC in ASD, particularly in the genu and splenium structures, potentially reflecting underlying pathophysiological mechanisms that warrant further investigation.
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Affiliation(s)
- Suvarna Badhe
- Department of Research and Development, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
- Department of Regenerative Laboratory, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Samson Nivins
- Department of Research and Development, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Pooja Kulkarni
- Department of Research and Development, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Alitta Jose
- Department of Research and Development, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Divesh Manek
- Department of Radiology, Omega MRI, Navi Mumbai, Maharashtra, India; and
| | - Satyendra Badhe
- Department of Research and Development, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
- Department of Regenerative Laboratory, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Hemangi Sane
- Department of Research and Development, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Nandini Gokulchandran
- Department of Medical Services and Clinical Research, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Prerna Badhe
- Department of Regenerative Laboratory, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
| | - Alok Sharma
- Department of Medical Services and Clinical Research, NeuroGen Brain and Spine Institute, Navi Mumbai, Maharashtra, India
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19
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Bhandari K, Kanodia H, Donato F, Caroni P. Selective vulnerability of the ventral hippocampus-prelimbic cortex axis parvalbumin interneuron network underlies learning deficits of fragile X mice. Cell Rep 2024; 43:114124. [PMID: 38630591 DOI: 10.1016/j.celrep.2024.114124] [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: 10/06/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
High-penetrance mutations affecting mental health can involve genes ubiquitously expressed in the brain. Whether the specific patterns of dysfunctions result from ubiquitous circuit deficits or might reflect selective vulnerabilities of targetable subnetworks has remained unclear. Here, we determine how loss of ubiquitously expressed fragile X mental retardation protein (FMRP), the cause of fragile X syndrome, affects brain networks in Fmr1y/- mice. We find that in wild-type mice, area-specific knockout of FMRP in the adult mimics behavioral consequences of area-specific silencing. By contrast, the functional axis linking the ventral hippocampus (vH) to the prelimbic cortex (PreL) is selectively affected in constitutive Fmr1y/- mice. A chronic alteration in late-born parvalbumin interneuron networks across the vH-PreL axis rescued by VIP signaling specifically accounts for deficits in vH-PreL theta-band network coherence, ensemble assembly, and learning functions of Fmr1y/- mice. Therefore, vH-PreL axis function exhibits a selective vulnerability to loss of FMRP in the vH or PreL, leading to learning and memory dysfunctions in fragile X mice.
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Affiliation(s)
- Komal Bhandari
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Harsh Kanodia
- Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Flavio Donato
- Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Pico Caroni
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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20
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Noguchi J, Watanabe S, Oga T, Isoda R, Nakagaki K, Sakai K, Sumida K, Hoshino K, Saito K, Miyawaki I, Sugano E, Tomita H, Mizukami H, Watakabe A, Yamamori T, Ichinohe N. Altered projection-specific synaptic remodeling and its modification by oxytocin in an idiopathic autism marmoset model. Commun Biol 2024; 7:642. [PMID: 38802535 PMCID: PMC11130163 DOI: 10.1038/s42003-024-06345-9] [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: 10/22/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Alterations in the experience-dependent and autonomous elaboration of neural circuits are assumed to underlie autism spectrum disorder (ASD), though it is unclear what synaptic traits are responsible. Here, utilizing a valproic acid-induced ASD marmoset model, which shares common molecular features with idiopathic ASD, we investigate changes in the structural dynamics of tuft dendrites of upper-layer pyramidal neurons and adjacent axons in the dorsomedial prefrontal cortex through two-photon microscopy. In model marmosets, dendritic spine turnover is upregulated, and spines are generated in clusters and survived more often than in control marmosets. Presynaptic boutons in local axons, but not in commissural long-range axons, demonstrate hyperdynamic turnover in model marmosets, suggesting alterations in projection-specific plasticity. Intriguingly, nasal oxytocin administration attenuates clustered spine emergence in model marmosets. Enhanced clustered spine generation, possibly unique to certain presynaptic partners, may be associated with ASD and be a potential therapeutic target.
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Affiliation(s)
- Jun Noguchi
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.
| | - Satoshi Watanabe
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Tomofumi Oga
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Risa Isoda
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Keiko Nakagaki
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Kazuhisa Sakai
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Kayo Sumida
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Osaka, Japan
| | - Kohei Hoshino
- Preclinical Research Laboratories, Sumitomo Pharma Co., Ltd., Osaka, Japan
| | - Koichi Saito
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Osaka, Japan
| | - Izuru Miyawaki
- Preclinical Research Laboratories, Sumitomo Pharma Co., Ltd., Osaka, Japan
| | - Eriko Sugano
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, Morioka, Japan
| | - Hiroshi Tomita
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, Morioka, Japan
| | - Hiroaki Mizukami
- Division of Genetic Therapeutics, Jichi Medical University, Shimotsuke, Japan
| | - Akiya Watakabe
- Laboratory for Molecular Analysis of Higher Brain Function, Center for Brain Science, RIKEN, Wako, Japan
| | - Tetsuo Yamamori
- Laboratory for Molecular Analysis of Higher Brain Function, Center for Brain Science, RIKEN, Wako, Japan
- Laboratory for Haptic Perception and Cognitive Physiology, Center for Brain Science, RIKEN, Wako, Japan
- Department of Marmoset Biology and Medicine, CIEM, Kawasaki, Japan
| | - Noritaka Ichinohe
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.
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21
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Nóbrega IDS, Teles e Silva AL, Yokota-Moreno BY, Sertié AL. The Importance of Large-Scale Genomic Studies to Unravel Genetic Risk Factors for Autism. Int J Mol Sci 2024; 25:5816. [PMID: 38892002 PMCID: PMC11172008 DOI: 10.3390/ijms25115816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Autism spectrum disorder (ASD) is a common and highly heritable neurodevelopmental disorder. During the last 15 years, advances in genomic technologies and the availability of increasingly large patient cohorts have greatly expanded our knowledge of the genetic architecture of ASD and its neurobiological mechanisms. Over two hundred risk regions and genes carrying rare de novo and transmitted high-impact variants have been identified. Additionally, common variants with small individual effect size are also important, and a number of loci are now being uncovered. At the same time, these new insights have highlighted ongoing challenges. In this perspective article, we summarize developments in ASD genetic research and address the enormous impact of large-scale genomic initiatives on ASD gene discovery.
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Affiliation(s)
| | | | | | - Andréa Laurato Sertié
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, Rua Comendador Elias Jafet, 755. Morumbi, São Paulo 05653-000, Brazil; (I.d.S.N.); (A.L.T.e.S.); (B.Y.Y.-M.)
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22
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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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23
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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] [Grants] [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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24
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Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science 2024; 384:eadh0829. [PMID: 38781368 DOI: 10.1126/science.adh0829] [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: 02/14/2023] [Accepted: 03/07/2024] [Indexed: 05/25/2024]
Abstract
Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanisms is challenging without a unified regulatory atlas. Across 672 diverse developing human brains, we identified 15,752 genes harboring gene, isoform, and/or splicing quantitative trait loci, mapping 3739 to cellular contexts. Gene expression heritability drops during development, likely reflecting both increasing cellular heterogeneity and the intrinsic properties of neuronal maturation. Isoform-level regulation, particularly in the second trimester, mediated the largest proportion of GWAS heritability. Through colocalization, we prioritized mechanisms for about 60% of GWAS loci across five disorders, exceeding adult brain findings. Finally, we contextualized results within gene and isoform coexpression networks, revealing the comprehensive landscape of transcriptome regulation in development and disease.
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Affiliation(s)
- Cindy Wen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, 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
| | - Michael Margolis
- Department of Psychiatry, 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
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Pan Zhang
- Department of Psychiatry, 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
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA
| | - Daniel D Vo
- Department of Psychiatry, 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
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Miao Tang
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chuan Jiao
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Team Krebs, 75014 Paris, France
| | - Minsoo Kim
- Department of Psychiatry, 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
| | - Ellen Tsai
- Department of Psychiatry, 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
| | - Celine Hoh
- Department of Psychiatry, 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
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca L Walker
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, 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
| | - Christos Chatzinakos
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- McLean Hospital, Belmont, MA 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Declan Clarke
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mette A Peters
- CNS Data Coordination Group, Sage Bionetworks, Seattle, WA 98109, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Nikolaos P Daskalakis
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- McLean Hospital, Belmont, MA 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Neumora Therapeutics, Watertown, MA 02472, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine, Cardiff CF24 4HQ, UK
| | - Nenad Sestan
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Daniel H Geschwind
- Department of Human Genetics, 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
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kathryn Roeder
- Department of Statistics & Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02215, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Bogdan Pasaniuc
- Interdepartmental Program in Bioinformatics, 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 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
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, 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
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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25
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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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26
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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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Xie X, Zhou R, Fang Z, Zhang Y, Wang Q, Liu X. Seeing beyond words: Visualizing autism spectrum disorder biomarker insights. Heliyon 2024; 10:e30420. [PMID: 38694128 PMCID: PMC11061761 DOI: 10.1016/j.heliyon.2024.e30420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024] Open
Abstract
Objective This study employs bibliometric and visual analysis to elucidate global research trends in Autism Spectrum Disorder (ASD) biomarkers, identify critical research focal points, and discuss the potential integration of diverse biomarker modalities for precise ASD assessment. Methods A comprehensive bibliometric analysis was conducted using data from the Web of Science Core Collection database until December 31, 2022. Visualization tools, including R, VOSviewer, CiteSpace, and gCLUTO, were utilized to examine collaborative networks, co-citation patterns, and keyword associations among countries, institutions, authors, journals, documents, and keywords. Results ASD biomarker research emerged in 2004, accumulating a corpus of 4348 documents by December 31, 2022. The United States, with 1574 publications and an H-index of 213, emerged as the most prolific and influential country. The University of California, Davis, contributed significantly with 346 publications and an H-index of 69, making it the leading institution. Concerning journals, the Journal of Autism and Developmental Disorders, Autism Research, and PLOS ONE were the top three publishers of ASD biomarker-related articles among a total of 1140 academic journals. Co-citation and keyword analyses revealed research hotspots in genetics, imaging, oxidative stress, neuroinflammation, gut microbiota, and eye tracking. Emerging topics included "DNA methylation," "eye tracking," "metabolomics," and "resting-state fMRI." Conclusion The field of ASD biomarker research is dynamically evolving. Future endeavors should prioritize individual stratification, methodological standardization, the harmonious integration of biomarker modalities, and longitudinal studies to advance the precision of ASD diagnosis and treatment.
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Affiliation(s)
- Xinyue Xie
- The First Affiliated Hospital of Henan University of Chinese Medicine, Pediatrics Hospital, Zhengzhou, Henan, 450000, China
- Henan University of Chinese Medicine, School of Pediatrics, Zhengzhou, Henan, 450046, China
| | - Rongyi Zhou
- The First Affiliated Hospital of Henan University of Chinese Medicine, Pediatrics Hospital, Zhengzhou, Henan, 450000, China
- Henan University of Chinese Medicine, School of Pediatrics, Zhengzhou, Henan, 450046, China
| | - Zihan Fang
- Henan University of Chinese Medicine, School of Pediatrics, Zhengzhou, Henan, 450046, China
| | - Yongting Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Pediatrics Hospital, Zhengzhou, Henan, 450000, China
- Henan University of Chinese Medicine, School of Pediatrics, Zhengzhou, Henan, 450046, China
| | - Qirong Wang
- Henan University of Chinese Medicine, School of Pediatrics, Zhengzhou, Henan, 450046, China
| | - Xiaomian Liu
- Henan University of Chinese Medicine, School of Medicine, Zhengzhou, Henan, 450046, China
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28
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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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29
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Akkouh IA, Ueland T, Szabo A, Hughes T, Smeland OB, Andreassen OA, Osete JR, Djurovic S. Longitudinal Transcriptomic Analysis of Human Cortical Spheroids Identifies Axonal Dysregulation in the Prenatal Brain as a Mediator of Genetic Risk for Schizophrenia. Biol Psychiatry 2024; 95:687-698. [PMID: 37661009 DOI: 10.1016/j.biopsych.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/28/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Schizophrenia (SCZ) has a known neurodevelopmental etiology, but limited access to human prenatal brain tissue hampers the investigation of basic disease mechanisms in early brain development. Here, we elucidate the molecular mechanisms contributing to SCZ risk in a disease-relevant model of the prenatal human brain. METHODS We generated induced pluripotent stem cell-derived organoids, termed human cortical spheroids (hCSs), from a large, genetically stratified sample of 14 SCZ cases and 14 age- and sex-matched controls. The hCSs were differentiated for 150 days, and comprehensive molecular characterization across 4 time points was carried out. RESULTS The transcriptional and cellular architecture of hCSs closely resembled that of fetal brain tissue at 10 to 24 postconception weeks, showing strongest spatial overlap with frontal regions of the cerebral cortex. A total of 3520 genes were differentially modulated between SCZ and control hCSs across organoid maturation, displaying a significant contribution of genetic loading, an overrepresentation of risk genes for autism spectrum disorder and SCZ, and the strongest enrichment for axonal processes in all hCS stages. The two axon guidance genes SEMA7A and SEMA5A, the first a promoter of synaptic functions and the second a repressor, were downregulated and upregulated, respectively, in SCZ hCSs. This expression pattern was confirmed at the protein level and replicated in a large postmortem sample. CONCLUSIONS Applying a disease-relevant model of the developing fetal brain, we identified consistent dysregulation of axonal genes as an early risk factor for SCZ, providing novel insights into the effects of genetic predisposition on the neurodevelopmental origins of the disorder.
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Affiliation(s)
- Ibrahim A Akkouh
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; K.G. Jebsen Thrombosis Research and Expertise Center, University of Tromsø, Tromsø, Norway
| | - Attila Szabo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Timothy Hughes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Olav B Smeland
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Jordi Requena Osete
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
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30
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Prem S, Dev B, Peng C, Mehta M, Alibutud R, Connacher RJ, St Thomas M, Zhou X, Matteson P, Xing J, Millonig JH, DiCicco-Bloom E. Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells. eLife 2024; 13:e82809. [PMID: 38525876 PMCID: PMC11003747 DOI: 10.7554/elife.82809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes, and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.
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Affiliation(s)
- Smrithi Prem
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
| | - Bharati Dev
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Cynthia Peng
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Monal Mehta
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityPiscatawayUnited States
| | - Rohan Alibutud
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - Robert J Connacher
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
| | - Madeline St Thomas
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Graduate Program in Neuroscience, Rutgers UniversityPiscatawayUnited States
| | - Xiaofeng Zhou
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
| | - Paul Matteson
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityPiscatawayUnited States
| | - Jinchuan Xing
- Department of Genetics, Rutgers UniversityPiscatawayUnited States
| | - James H Millonig
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityPiscatawayUnited States
| | - Emanuel DiCicco-Bloom
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical SchoolPiscatawayUnited States
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical SchoolNew BrunswickUnited States
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31
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Chen GT, Nair G, Osorio AJ, Holley SM, Ghassemzadeh K, Gonzalez J, Lu C, Sanjana NE, Cepeda C, Geschwind DH. Enhancer-targeted CRISPR-Activation Rescues Haploinsufficient Autism Susceptibility Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584921. [PMID: 38559217 PMCID: PMC10980046 DOI: 10.1101/2024.03.13.584921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Autism Spectrum Disorder (ASD) is a highly heritable condition with diverse clinical presentations. Approximately 20% of ASD's genetic susceptibility is imparted by de novo mutations of major effect, most of which cause haploinsufficiency. We mapped enhancers of two high confidence autism genes - CHD8 and SCN2A and used CRISPR-based gene activation (CRISPR-A) in hPSC-derived excitatory neurons and cerebral forebrain organoids to correct the effects of haploinsufficiency, taking advantage of the presence of a wildtype allele of each gene and endogenous gene regulation. We found that CRISPR-A induced a sustained increase in CHD8 and SCN2A expression in treated neurons and organoids, with rescue of gene expression levels and mutation-associated phenotypes, including gene expression and physiology. These data support gene activation via targeting enhancers of haploinsufficient genes, as a therapeutic intervention in ASD and other neurodevelopmental disorders.
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32
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Tian Y, Yu F, Yun E, Lin JW, Man HY. mRNA nuclear retention reduces AMPAR expression and promotes autistic behavior in UBE3A-overexpressing mice. EMBO Rep 2024; 25:1282-1309. [PMID: 38316900 PMCID: PMC10933332 DOI: 10.1038/s44319-024-00073-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/07/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
UBE3A is a common genetic factor in ASD etiology, and transgenic mice overexpressing UBE3A exhibit typical autistic-like behaviors. Because AMPA receptors (AMPARs) mediate most of the excitatory synaptic transmission in the brain, and synaptic dysregulation is considered one of the primary cellular mechanisms in ASD pathology, we investigate here the involvement of AMPARs in UBE3A-dependent ASD. We show that expression of the AMPAR GluA1 subunit is decreased in UBE3A-overexpressing mice, and that AMPAR-mediated neuronal activity is reduced. GluA1 mRNA is trapped in the nucleus of UBE3A-overexpressing neurons, suppressing GluA1 protein synthesis. Also, SARNP, an mRNA nuclear export protein, is downregulated in UBE3A-overexpressing neurons, causing GluA1 mRNA nuclear retention. Restoring SARNP levels not only rescues GluA1 mRNA localization and protein expression, but also normalizes neuronal activity and autistic behaviors in mice overexpressing UBE3A. These findings indicate that SARNP plays a crucial role in the cellular and behavioral phenotypes of UBE3A-induced ASD by regulating nuclear mRNA trafficking and protein translation of a key AMPAR subunit.
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Affiliation(s)
- Yuan Tian
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Feiyuan Yu
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Eunice Yun
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Jen-Wei Lin
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - Heng-Ye Man
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
- Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Center for Systems Neuroscience, Boston University, 610 Commonwealth Avenue, Boston, MA, 02215, USA.
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33
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Vacharasin JM, Ward JA, McCord MM, Cox K, Imitola J, Lizarraga SB. Neuroimmune mechanisms in autism etiology - untangling a complex problem using human cellular models. OXFORD OPEN NEUROSCIENCE 2024; 3:kvae003. [PMID: 38665176 PMCID: PMC11044813 DOI: 10.1093/oons/kvae003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 04/28/2024]
Abstract
Autism spectrum disorder (ASD) affects 1 in 36 people and is more often diagnosed in males than in females. Core features of ASD are impaired social interactions, repetitive behaviors and deficits in verbal communication. ASD is a highly heterogeneous and heritable disorder, yet its underlying genetic causes account only for up to 80% of the cases. Hence, a subset of ASD cases could be influenced by environmental risk factors. Maternal immune activation (MIA) is a response to inflammation during pregnancy, which can lead to increased inflammatory signals to the fetus. Inflammatory signals can cross the placenta and blood brain barriers affecting fetal brain development. Epidemiological and animal studies suggest that MIA could contribute to ASD etiology. However, human mechanistic studies have been hindered by a lack of experimental systems that could replicate the impact of MIA during fetal development. Therefore, mechanisms altered by inflammation during human pre-natal brain development, and that could underlie ASD pathogenesis have been largely understudied. The advent of human cellular models with induced pluripotent stem cell (iPSC) and organoid technology is closing this gap in knowledge by providing both access to molecular manipulations and culturing capability of tissue that would be otherwise inaccessible. We present an overview of multiple levels of evidence from clinical, epidemiological, and cellular studies that provide a potential link between higher ASD risk and inflammation. More importantly, we discuss how stem cell-derived models may constitute an ideal experimental system to mechanistically interrogate the effect of inflammation during the early stages of brain development.
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Affiliation(s)
- Janay M Vacharasin
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
- Department of Biological Sciences, Francis Marion University, 4822 East Palmetto Street, Florence, S.C. 29506, USA
| | - Joseph A Ward
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute of Brain Science, Brown University, 70 Ship Street, Providence, RI 02903, USA
| | - Mikayla M McCord
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Kaitlin Cox
- Department of Biological Sciences, and Center for Childhood Neurotherapeutics, Univ. of South Carolina, 715 Sumter Street, Columbia, SC 29208, USA
| | - Jaime Imitola
- Laboratory of Neural Stem Cells and Functional Neurogenetics, UConn Health, Departments of Neuroscience, Neurology, Genetics and Genome Sciences, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-5357, USA
| | - Sofia B Lizarraga
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute of Brain Science, Brown University, 70 Ship Street, Providence, RI 02903, USA
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34
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Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569805. [PMID: 38076945 PMCID: PMC10705567 DOI: 10.1101/2023.12.03.569805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.
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35
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Wagstyl K, Adler S, Seidlitz J, Vandekar S, Mallard TT, Dear R, DeCasien AR, Satterthwaite TD, Liu S, Vértes PE, Shinohara RT, Alexander-Bloch A, Geschwind DH, Raznahan A. Transcriptional cartography integrates multiscale biology of the human cortex. eLife 2024; 12:RP86933. [PMID: 38324465 PMCID: PMC10945526 DOI: 10.7554/elife.86933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
The cerebral cortex underlies many of our unique strengths and vulnerabilities, but efforts to understand human cortical organization are challenged by reliance on incompatible measurement methods at different spatial scales. Macroscale features such as cortical folding and functional activation are accessed through spatially dense neuroimaging maps, whereas microscale cellular and molecular features are typically measured with sparse postmortem sampling. Here, we integrate these distinct windows on brain organization by building upon existing postmortem data to impute, validate, and analyze a library of spatially dense neuroimaging-like maps of human cortical gene expression. These maps allow spatially unbiased discovery of cortical zones with extreme transcriptional profiles or unusually rapid transcriptional change which index distinct microstructure and predict neuroimaging measures of cortical folding and functional activation. Modules of spatially coexpressed genes define a family of canonical expression maps that integrate diverse spatial scales and temporal epochs of human brain organization - ranging from protein-protein interactions to large-scale systems for cognitive processing. These module maps also parse neuropsychiatric risk genes into subsets which tag distinct cyto-laminar features and differentially predict the location of altered cortical anatomy and gene expression in patients. Taken together, the methods, resources, and findings described here advance our understanding of human cortical organization and offer flexible bridges to connect scientific fields operating at different spatial scales of human brain research.
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Affiliation(s)
- Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, University College LondonLondonUnited Kingdom
| | - Sophie Adler
- UCL Great Ormond Street Institute for Child HealthHolbornUnited Kingdom
| | - Jakob Seidlitz
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Simon Vandekar
- Department of Biostatistics, Vanderbilt UniversityNashvilleUnited States
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Psychiatry, Harvard Medical SchoolBostonUnited States
| | - Richard Dear
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Alex R DeCasien
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Theodore D Satterthwaite
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of MedicinePhiladelphiaUnited States
| | - Siyuan Liu
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Petra E Vértes
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
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Basu S, Ro EJ, Liu Z, Kim H, Bennett A, Kang S, Suh H. The Mef2c Gene Dose-Dependently Controls Hippocampal Neurogenesis and the Expression of Autism-Like Behaviors. J Neurosci 2024; 44:e1058232023. [PMID: 38123360 PMCID: PMC10860657 DOI: 10.1523/jneurosci.1058-23.2023] [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: 05/29/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Mutations in the activity-dependent transcription factor MEF2C have been associated with several neuropsychiatric disorders. Among these, autism spectrum disorder (ASD)-related behavioral deficits are manifested. Multiple animal models that harbor mutations in Mef2c have provided compelling evidence that Mef2c is indeed an ASD gene. However, studies in mice with germline or global brain knock-out of Mef2c are limited in their ability to identify the precise neural substrates and cell types that are required for the expression of Mef2c-mediated ASD behaviors. Given the role of hippocampal neurogenesis in cognitive and social behaviors, in this study we aimed to investigate the role of Mef2c in the structure and function of newly generated dentate granule cells (DGCs) in the postnatal hippocampus and to determine whether disrupted Mef2c function is responsible for manifesting ASD behaviors. Overexpression of Mef2c (Mef2cOE ) arrested the transition of neurogenesis at progenitor stages, as indicated by sustained expression of Sox2+ in Mef2cOE DGCs. Conditional knock-out of Mef2c (Mef2ccko ) allowed neuronal commitment of Mef2ccko cells; however, Mef2ccko impaired not only dendritic arborization and spine formation but also synaptic transmission onto Mef2ccko DGCs. Moreover, the abnormal structure and function of Mef2ccko DGCs led to deficits in social interaction and social novelty recognition, which are key characteristics of ASD behaviors. Thus, our study revealed a dose-dependent requirement of Mef2c in the control of distinct steps of neurogenesis, as well as a critical cell-autonomous function of Mef2c in newborn DGCs in the expression of proper social behavior in both sexes.
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Affiliation(s)
- Sreetama Basu
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
| | - Eun Jeoung Ro
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
| | - Zhi Liu
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
| | - Hyunjung Kim
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta 30912, Georgia
| | - Aubrey Bennett
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta 30912, Georgia
| | - Seungwoo Kang
- Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, Augusta 30912, Georgia
| | - Hoonkyo Suh
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland 44109, Ohio
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Wang H, Chang TS, Dombroski BA, Cheng PL, Patil V, Valiente-Banuet L, Farrell K, Mclean C, Molina-Porcel L, Rajput A, De Deyn PP, Bastard NL, Gearing M, Kaat LD, Swieten JCV, Dopper E, Ghetti BF, Newell KL, Troakes C, de Yébenes JG, Rábano-Gutierrez A, Meller T, Oertel WH, Respondek G, Stamelou M, Arzberger T, Roeber S, Müller U, Hopfner F, Pastor P, Brice A, Durr A, Ber IL, Beach TG, Serrano GE, Hazrati LN, Litvan I, Rademakers R, Ross OA, Galasko D, Boxer AL, Miller BL, Seeley WW, Deerlin VMV, Lee EB, White CL, Morris H, de Silva R, Crary JF, Goate AM, Friedman JS, Leung YY, Coppola G, Naj AC, Wang LS, Dickson DW, Höglinger GU, Schellenberg GD, Geschwind DH, Lee WP. Whole-Genome Sequencing Analysis Reveals New Susceptibility Loci and Structural Variants Associated with Progressive Supranuclear Palsy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.12.28.23300612. [PMID: 38234807 PMCID: PMC10793533 DOI: 10.1101/2023.12.28.23300612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Progressive supranuclear palsy (PSP) is a rare neurodegenerative disease characterized by the accumulation of aggregated tau proteins in astrocytes, neurons, and oligodendrocytes. Previous genome-wide association studies for PSP were based on genotype array, therefore, were inadequate for the analysis of rare variants as well as larger mutations, such as small insertions/deletions (indels) and structural variants (SVs). Method In this study, we performed whole genome sequencing (WGS) and conducted association analysis for single nucleotide variants (SNVs), indels, and SVs, in a cohort of 1,718 cases and 2,944 controls of European ancestry. Of the 1,718 PSP individuals, 1,441 were autopsy-confirmed and 277 were clinically diagnosed. Results Our analysis of common SNVs and indels confirmed known genetic loci at MAPT, MOBP, STX6, SLCO1A2, DUSP10, and SP1, and further uncovered novel signals in APOE, FCHO1/MAP1S, KIF13A, TRIM24, TNXB, and ELOVL1. Notably, in contrast to Alzheimer's disease (AD), we observed the APOE ε2 allele to be the risk allele in PSP. Analysis of rare SNVs and indels identified significant association in ZNF592 and further gene network analysis identified a module of neuronal genes dysregulated in PSP. Moreover, seven common SVs associated with PSP were observed in the H1/H2 haplotype region (17q21.31) and other loci, including IGH, PCMT1, CYP2A13, and SMCP. In the H1/H2 haplotype region, there is a burden of rare deletions and duplications (P = 6.73×10-3) in PSP. Conclusions Through WGS, we significantly enhanced our understanding of the genetic basis of PSP, providing new targets for exploring disease mechanisms and therapeutic interventions.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy S Chang
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vishakha Patil
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Leopoldo Valiente-Banuet
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kurt Farrell
- Department of Pathology, Department of Artificial Intelligence & Human Health, Nash Family, Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain, Institute, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catriona Mclean
- Victorian Brain Bank, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Laura Molina-Porcel
- Alzheimer's disease and other cognitive disorders unit. Neurology Service, Hospital Clínic, Fundació Recerca Clínic Barcelona (FRCB). Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Neurological Tissue Bank of the Biobanc-Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Alex Rajput
- Movement Disorders Program, Division of Neurology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Peter Paul De Deyn
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, University of Antwerp, Wilrijk (Antwerp), Belgium
- Department of Neurology, University Medical Center Groningen, NL-9713 AV Groningen, Netherlands
| | | | - Marla Gearing
- Department of Pathology and Laboratory Medicine and Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Elise Dopper
- Netherlands Brain Bank and Erasmus University, Netherlands
| | - Bernardino F Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | | | - Alberto Rábano-Gutierrez
- Fundación CIEN (Centro de Investigación de Enfermedades Neurológicas) - Centro Alzheimer Fundación Reina Sofía, Madrid, Spain
| | - Tina Meller
- Department of Neurology, Philipps-Universität, Marburg, Germany
| | | | - Gesine Respondek
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Maria Stamelou
- Parkinson's disease and Movement Disorders Department, HYGEIA Hospital, Athens, Greece
- European University of Cyprus, Nicosia, Cyprus
| | - Thomas Arzberger
- Department of Psychiatry and Psychotherapy, University Hospital Munich, Ludwig-Maximilians-University Munich, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Germany
| | | | | | - Franziska Hopfner
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pau Pastor
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
- Neurosciences, The Germans Trias i Pujol Research Institute (IGTP) Badalona, Badalona, Spain
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Isabelle Le Ber
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | | | - Irene Litvan
- Department of Neuroscience, University of California, San Diego, CA, USA
| | - Rosa Rademakers
- VIB Center for Molecular Neurology, University of Antwerp, Belgium
- Department of Neuroscience, Mayo Clinic Jacksonville, FL, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic Jacksonville, FL, USA
| | - Douglas Galasko
- Department of Neuroscience, University of California, San Diego, CA, USA
| | - Adam L Boxer
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Bruce L Miller
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Willian W Seeley
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Vivanna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charles L White
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huw Morris
- Departmento of Clinical and Movement Neuroscience, University College of London, London, UK
| | - Rohan de Silva
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - John F Crary
- Department of Pathology, Department of Artificial Intelligence & Human Health, Nash Family, Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain, Institute, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey S Friedman
- Friedman Bioventure, Inc., Del Mar, CA, USA; Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giovanni Coppola
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Günter U Höglinger
- Department of Neurology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) München; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel H Geschwind
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Faraji R, Ganji Z, Khandan Khadem Z, Akbari-Lalimi H, Eidy F, Zare H. Volume-based and Surface-Based Methods in Autism Compared with Healthy Controls Are Free surfer and CAT12 in Agreement? IRANIAN JOURNAL OF CHILD NEUROLOGY 2024; 18:93-118. [PMID: 38375127 PMCID: PMC10874516 DOI: 10.22037/ijcn.v18i1.43294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/07/2023] [Indexed: 02/21/2024]
Abstract
Objectives Autism Spectrum Disorder (ASD) encompasses a range of neurodevelopmental disorders, and early detection is crucial. This study aims to identify the Regions of Interest (ROIs) with significant differences between healthy controls and individuals with autism, as well as evaluate the agreement between FreeSurfer 6 (FS6) and Computational Anatomy Toolbox (CAT12) methods. Materials & Methods Surface-based and volume-based features were extracted from FS software and CAT12 toolbox for Statistical Parametric Mapping (SPM) software to estimate ROI-wise biomarkers. These biomarkers were compared between 18 males Typically Developing Controls (TDCs) and 40 male subjects with ASD to assess group differences for each method. Finally, agreement and regression analyses were performed between the two methods for TDCs and ASD groups. Results Both methods revealed ROIs with significant differences for each parameter. The Analysis of Covariance (ANCOVA) showed that both TDCs and ASD groups indicated a significant relationship between the two methods (p<0.001). The R2 values for TDCs and ASD groups were 0.692 and 0.680, respectively, demonstrating a moderate correlation between CAT12 and FS6. Bland-Altman graphs showed a moderate level of agreement between the two methods. Conclusion The moderate correlation and agreement between CAT12 and FS6 suggest that while some consistency is observed in the results, CAT12 is not a superior substitute for FS6 software. Further research is needed to identify a potential replacement for this method.
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Affiliation(s)
- Reyhane Faraji
- Medical Physics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zohreh Ganji
- Medical Physics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khandan Khadem
- Medical Physics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Akbari-Lalimi
- Medical Physics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fereshteh Eidy
- Department of Biostatistics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hoda Zare
- Medical Physics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Physics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Bar O, Vahey E, Mintz M, Frye RE, Boles RG. Reanalysis of Trio Whole-Genome Sequencing Data Doubles the Yield in Autism Spectrum Disorder: De Novo Variants Present in Half. Int J Mol Sci 2024; 25:1192. [PMID: 38256266 PMCID: PMC10816071 DOI: 10.3390/ijms25021192] [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: 12/24/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Autism spectrum disorder (ASD) is a common condition with lifelong implications. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole-genome sequencing (trio-WGS). "Qualified" variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV), additionally, were present in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes (p = 0.0002), validating that most are indeed disease related. Sequence reanalysis increased diagnostic yield from 28% to 68%, mostly through inclusion of de novo PDVs in genes not yet reported as ASD associated. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate a high yield of trio-WGS for revealing molecular diagnoses in ASD, which is greatly enhanced by reanalyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism.
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Affiliation(s)
- Omri Bar
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
| | - Elizabeth Vahey
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
| | - Mark Mintz
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
| | - Richard E. Frye
- Autism Discovery and Treatment Foundation, Phoenix, AZ 85050, USA;
| | - Richard G. Boles
- NeurAbilities Healthcare, Voorhees, NJ 08043, USA; (O.B.); (E.V.); (M.M.)
- NeuroNeeds, Old Lyme, CT 06371, USA
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McClellan JM, Zoghbi AW, Buxbaum JD, Cappi C, Crowley JJ, Flint J, Grice DE, Gulsuner S, Iyegbe C, Jain S, Kuo PH, Lattig MC, Passos-Bueno MR, Purushottam M, Stein DJ, Sunshine AB, Susser ES, Walsh CA, Wootton O, King MC. An evolutionary perspective on complex neuropsychiatric disease. Neuron 2024; 112:7-24. [PMID: 38016473 PMCID: PMC10842497 DOI: 10.1016/j.neuron.2023.10.037] [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: 08/02/2022] [Revised: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Flint
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | | | | | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Anna B Sunshine
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ezra S Susser
- Department of Epidemiology, Mailman School of Public Health, and New York State Psychiatric Institute, Columbia University, New York, NY 10032, USA
| | - Christopher A Walsh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Wootton
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Sun N, Teyssier N, Wang B, Drake S, Seyler M, Zaltsman Y, Everitt A, Teerikorpi N, Willsey HR, Goodarzi H, Tian R, Kampmann M, Willsey AJ. Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.573108. [PMID: 38187634 PMCID: PMC10769323 DOI: 10.1101/2023.12.22.573108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent studies have identified over one hundred high-confidence (hc) autism spectrum disorder (ASD) genes. Systems biological and functional analyses on smaller subsets of these genes have consistently implicated excitatory neurogenesis. However, the extent to which the broader set of hcASD genes are involved in this process has not been explored systematically nor have the biological pathways underlying this convergence been identified. Here, we leveraged CROP-Seq to repress 87 hcASD genes in a human in vitro model of cortical neurogenesis. We identified 17 hcASD genes whose repression significantly alters developmental trajectory and results in a common cellular state characterized by disruptions in proliferation, differentiation, cell cycle, microtubule biology, and RNA-binding proteins (RBPs). We also characterized over 3,000 differentially expressed genes, 286 of which had expression profiles correlated with changes in developmental trajectory. Overall, we uncovered transcriptional disruptions downstream of hcASD gene perturbations, correlated these disruptions with distinct differentiation phenotypes, and reinforced neurogenesis, microtubule biology, and RBPs as convergent points of disruption in ASD.
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Di Gesù CM, Buffington SA. The early life exposome and autism risk: a role for the maternal microbiome? Gut Microbes 2024; 16:2385117. [PMID: 39120056 PMCID: PMC11318715 DOI: 10.1080/19490976.2024.2385117] [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: 04/01/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
Autism spectrum disorders (ASD) are highly heritable, heterogeneous neurodevelopmental disorders characterized by clinical presentation of atypical social, communicative, and repetitive behaviors. Over the past 25 years, hundreds of ASD risk genes have been identified. Many converge on key molecular pathways, from translational control to those regulating synaptic structure and function. Despite these advances, therapeutic approaches remain elusive. Emerging data unearthing the relationship between genetics, microbes, and immunity in ASD suggest an integrative physiology approach could be paramount to delivering therapeutic breakthroughs. Indeed, the advent of large-scale multi-OMIC data acquisition, analysis, and interpretation is yielding an increasingly mechanistic understanding of ASD and underlying risk factors, revealing how genetic susceptibility interacts with microbial genetics, metabolism, epigenetic (re)programming, and immunity to influence neurodevelopment and behavioral outcomes. It is now possible to foresee exciting advancements in the treatment of some forms of ASD that could markedly improve quality of life and productivity for autistic individuals. Here, we highlight recent work revealing how gene X maternal exposome interactions influence risk for ASD, with emphasis on the intrauterine environment and fetal neurodevelopment, host-microbe interactions, and the evolving therapeutic landscape for ASD.
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Affiliation(s)
- Claudia M. Di Gesù
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Shelly A. Buffington
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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43
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Li WK, Zhang SQ, Peng WL, Shi YH, Yuan B, Yuan YT, Xue ZY, Wang JC, Han WJ, Chen ZF, Shan SF, Xue BQ, Chen JL, Zhang C, Zhu SJ, Tai YL, Cheng TL, Qiu ZL. Whole-brain in vivo base editing reverses behavioral changes in Mef2c-mutant mice. Nat Neurosci 2024; 27:116-128. [PMID: 38012399 DOI: 10.1038/s41593-023-01499-x] [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: 10/23/2022] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
Whole-brain genome editing to correct single-base mutations and reduce or reverse behavioral changes in animal models of autism spectrum disorder (ASD) has not yet been achieved. We developed an apolipoprotein B messenger RNA-editing enzyme, catalytic polypeptide-embedded cytosine base editor (AeCBE) system for converting C·G to T·A base pairs. We demonstrate its effectiveness by targeting AeCBE to an ASD-associated mutation of the MEF2C gene (c.104T>C, p.L35P) in vivo in mice. We first constructed Mef2cL35P heterozygous mice. Male heterozygous mice exhibited hyperactivity, repetitive behavior and social abnormalities. We then programmed AeCBE to edit the mutated C·G base pairs of Mef2c in the mouse brain through the intravenous injection of blood-brain barrier-crossing adeno-associated virus. This treatment successfully restored Mef2c protein levels in several brain regions and reversed the behavioral abnormalities in Mef2c-mutant mice. Our work presents an in vivo base-editing paradigm that could potentially correct single-base genetic mutations in the brain.
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Affiliation(s)
- Wei-Ke Li
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shu-Qian Zhang
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Wan-Ling Peng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Han Shi
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bo Yuan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Ting Yuan
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen-Yu Xue
- Department of Anesthesiology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin-Cheng Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Wen-Jian Han
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Fang Chen
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Shi-Fang Shan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Bi-Qing Xue
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jin-Long Chen
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Cheng Zhang
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shu-Jia Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Lin Tai
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Ministry of Education Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tian-Lin Cheng
- Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
| | - Zi-Long Qiu
- Songjiang Research Institute, Songjiang Hospital & MOE-Shanghai Key Laboratory for Children's Environmental Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Clinical Neuroscience Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
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Kiziltug E, Duy PQ, Allington G, Timberlake AT, Kawaguchi R, Long AS, Almeida MN, DiLuna ML, Alper SL, Alperovich M, Geschwind DH, Kahle KT. Concurrent impact of de novo mutations on cranial and cortical development in nonsyndromic craniosynostosis. J Neurosurg Pediatr 2024; 33:59-72. [PMID: 37890181 PMCID: PMC10783441 DOI: 10.3171/2023.8.peds23155] [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: 04/03/2023] [Accepted: 08/17/2023] [Indexed: 10/29/2023]
Abstract
OBJECTIVE Nonsyndromic craniosynostosis (nsCS), characterized by premature cranial suture fusion, is considered a primary skull disorder in which impact on neurodevelopment, if present, results from the mechanical hindrance of brain growth. Despite surgical repair of the cranial defect, neurocognitive deficits persist in nearly half of affected children. Therefore, the authors performed a functional genomics analysis of nsCS to determine when, where, and in what cell types nsCS-associated genes converge during development. METHODS The authors integrated whole-exome sequencing data from 291 nsCS proband-parent trios with 29,803 single-cell transcriptomes of the prenatal and postnatal neurocranial complex to inform when, where, and in what cell types nsCS-mutated genes might exert their pathophysiological effects. RESULTS The authors found that nsCS-mutated genes converged in cranial osteoprogenitors and pial fibroblasts and their transcriptional networks that regulate both skull ossification and cerebral neurogenesis. Nonsyndromic CS-mutated genes also converged in inhibitory neurons and gene coexpression modules that overlapped with autism and other developmental disorders. Ligand-receptor cell-cell communication analysis uncovered crosstalk between suture osteoblasts and neurons via the nsCS-associated BMP, FGF, and noncanonical WNT signaling pathways. CONCLUSIONS These data implicate a concurrent impact of nsCS-associated de novo mutations on cranial morphogenesis and cortical development via cell- and non-cell-autonomous mechanisms in a developmental nexus of fetal osteoblasts, pial fibroblasts, and neurons. These results suggest that neurodevelopmental outcomes in nsCS patients may be driven more by mutational status than surgical technique.
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Affiliation(s)
- Emre Kiziltug
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Phan Q. Duy
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Garrett Allington
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Andrew T. Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, New York
| | - Riki Kawaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Aaron S. Long
- Department of Surgery, Division of Plastic Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Mariana N. Almeida
- Department of Surgery, Division of Plastic Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Michael L. DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Seth L. Alper
- Department of Medicine, Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Michael Alperovich
- Department of Surgery, Division of Plastic Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Daniel H. Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Kristopher T. Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; and
- Harvard Center for Developmental Brain Disorders, Massachusetts General Hospital, Boston, Massachusetts
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45
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Fan G, Ma J, Ma R, Suo M, Chen Y, Zhang S, Zeng Y, Chen Y. Microglia Modulate Neurodevelopment in Autism Spectrum Disorder and Schizophrenia. Int J Mol Sci 2023; 24:17297. [PMID: 38139124 PMCID: PMC10743577 DOI: 10.3390/ijms242417297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) include various neurological disorders with high genetic heterogeneity, characterized by delayed or impaired cognition, communication, adaptive behavior, and psychomotor skills. These disorders result in significant morbidity for children, thus burdening families and healthcare/educational systems. However, there is a lack of early diagnosis and effective therapies. Therefore, a more connected approach is required to explore these disorders. Microglia, the primary phagocytic cells within the central nervous system, are crucial in regulating neuronal viability, influencing synaptic dynamics, and determining neurodevelopmental outcomes. Although the neurobiological basis of autism spectrum disorder (ASD) and schizophrenia (SZ) has attracted attention in recent decades, the role of microglia in ASD and SZ remains unclear and requires further discussion. In this review, the important and frequently multifaceted roles that microglia play during neurodevelopment are meticulously emphasized and potential microglial mechanisms that might be involved in conditions such as ASD and SZ are postulated. It is of utmost importance to acquire a comprehensive understanding of the complexities of the interplay between microglia and neurons to design effective, targeted therapeutic strategies to mitigate the effects of NDDs.
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Affiliation(s)
| | | | | | | | | | | | - Yan Zeng
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Yushan Chen
- Brain Science and Advanced Technology Institute, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
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Jiang M, Wang Z, Lu T, Li X, Yang K, Zhao L, Zhang D, Li J, Wang L. Integrative analysis of long noncoding RNAs dysregulation and synapse-associated ceRNA regulatory axes in autism. Transl Psychiatry 2023; 13:375. [PMID: 38057311 DOI: 10.1038/s41398-023-02662-5] [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: 04/09/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex disorder of neurodevelopment, the function of long noncoding RNA (lncRNA) in ASD remains essentially unknown. In the present study, gene networks were used to explore the ASD disease mechanisms integrating multiple data types (for example, RNA expression, whole-exome sequencing signals, weighted gene co-expression network analysis, and protein-protein interaction) and datasets (five human postmortem datasets). A total of 388 lncRNAs and five co-expression modules were found to be altered in ASD. The downregulated co-expression M4 module was significantly correlated with ASD, enriched with autism susceptibility genes and synaptic signaling. Integrating lncRNAs from the M4 module and microRNA (miRNA) dysregulation data from the literature identified competing endogenous RNA (ceRNA) network. We identified the downregulated mRNAs that interact with miRNAs by the miRTarBase, miRDB, and TargetScan databases. Our analysis reveals that MIR600HG was downregulated in multiple brain tissue datasets and was closely associated with 9 autism-susceptible miRNAs in the ceRNA network. MIR600HG and target mRNAs (EPHA4, MOAP1, MAP3K9, STXBP1, PRKCE, and SCAMP5) were downregulated in the peripheral blood by quantitative reverse transcription polymerase chain reaction analysis (false discovery rate <0.05). Subsequently, we assessed the role of lncRNA dysregulation in altered mRNA levels. Experimental verification showed that some synapse-associated mRNAs were downregulated after the MIR600HG knockdown. BrainSpan project showed that the expression patterns of MIR600HG (primate-specific lncRNA) and synapse-associated mRNA were similar in different human brain regions and at different stages of development. A combination of support vector machine and random forest machine learning algorithms retrieved the marker gene for ASD in the ceRNA network, and the area under the curve of the diagnostic nomogram was 0.851. In conclusion, dysregulation of MIR600HG, a novel specific lncRNA associated with ASD, is responsible for the ASD-associated miRNA-mRNA axes, thereby potentially regulating synaptogenesis.
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Affiliation(s)
- Miaomiao Jiang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Ziqi Wang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Tianlan Lu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Xianjing Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Kang Yang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Liyang Zhao
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Dai Zhang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation (IBRR), South China Normal University, Guangzhou, China
| | - Jun Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.
| | - Lifang Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.
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López-Tobón A, Shyti R, Villa CE, Cheroni C, Fuentes-Bravo P, Trattaro S, Caporale N, Troglio F, Tenderini E, Mihailovich M, Skaros A, Gibson WT, Cuomo A, Bonaldi T, Mercurio C, Varasi M, Osborne L, Testa G. GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders. SCIENCE ADVANCES 2023; 9:eadh2726. [PMID: 38019906 PMCID: PMC10686562 DOI: 10.1126/sciadv.adh2726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Copy number variations at 7q11.23 cause neurodevelopmental disorders with shared and opposite manifestations. Deletion causes Williams-Beuren syndrome featuring hypersociability, while duplication causes 7q11.23 microduplication syndrome (7Dup), frequently exhibiting autism spectrum disorder (ASD). Converging evidence indicates GTF2I as key mediator of the cognitive-behavioral phenotypes, yet its role in cortical development and behavioral hallmarks remains largely unknown. We integrated proteomic and transcriptomic profiling of patient-derived cortical organoids, including longitudinally at single-cell resolution, to dissect 7q11.23 dosage-dependent and GTF2I-specific disease mechanisms. We observed dosage-dependent impaired dynamics of neural progenitor proliferation, transcriptional imbalances, and highly specific alterations in neuronal output, leading to precocious excitatory neuron production in 7Dup, which was rescued by restoring physiological GTF2I levels. Transgenic mice with Gtf2i duplication recapitulated progenitor proliferation and neuronal differentiation defects alongside ASD-like behaviors. Consistently, inhibition of lysine demethylase 1 (LSD1), a GTF2I effector, was sufficient to rescue ASD-like phenotypes in transgenic mice, establishing GTF2I-LSD1 axis as a molecular pathway amenable to therapeutic intervention in ASD.
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Affiliation(s)
- Alejandro López-Tobón
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Reinald Shyti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Carlo Emanuele Villa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Patricio Fuentes-Bravo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sebastiano Trattaro
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicolò Caporale
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Flavia Troglio
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Erika Tenderini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Adrianos Skaros
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - William T. Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Mario Varasi
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Lucy Osborne
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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48
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Bhaskaran AA, Gauvrit T, Vyas Y, Bony G, Ginger M, Frick A. Endogenous noise of neocortical neurons correlates with atypical sensory response variability in the Fmr1 -/y mouse model of autism. Nat Commun 2023; 14:7905. [PMID: 38036566 PMCID: PMC10689491 DOI: 10.1038/s41467-023-43777-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
Excessive neural variability of sensory responses is a hallmark of atypical sensory processing in autistic individuals with cascading effects on other core autism symptoms but unknown neurobiological substrate. Here, by recording neocortical single neuron activity in a well-established mouse model of Fragile X syndrome and autism, we characterized atypical sensory processing and probed the role of endogenous noise sources in exaggerated response variability in males. The analysis of sensory stimulus evoked activity and spontaneous dynamics, as well as neuronal features, reveals a complex cellular and network phenotype. Neocortical sensory information processing is more variable and temporally imprecise. Increased trial-by-trial and inter-neuronal response variability is strongly related to key endogenous noise features, and may give rise to behavioural sensory responsiveness variability in autism. We provide a novel preclinical framework for understanding the sources of endogenous noise and its contribution to core autism symptoms, and for testing the functional consequences for mechanism-based manipulation of noise.
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Affiliation(s)
- Arjun A Bhaskaran
- INSERM, U1215 Neurocentre Magendie, 33077, Bordeaux, France
- University of Bordeaux, 33000, Bordeaux, France
- Department of Psychiatry, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Théo Gauvrit
- INSERM, U1215 Neurocentre Magendie, 33077, Bordeaux, France
- University of Bordeaux, 33000, Bordeaux, France
| | - Yukti Vyas
- INSERM, U1215 Neurocentre Magendie, 33077, Bordeaux, France
- University of Bordeaux, 33000, Bordeaux, France
| | - Guillaume Bony
- INSERM, U1215 Neurocentre Magendie, 33077, Bordeaux, France
- University of Bordeaux, 33000, Bordeaux, France
| | - Melanie Ginger
- INSERM, U1215 Neurocentre Magendie, 33077, Bordeaux, France
- University of Bordeaux, 33000, Bordeaux, France
| | - Andreas Frick
- INSERM, U1215 Neurocentre Magendie, 33077, Bordeaux, France.
- University of Bordeaux, 33000, Bordeaux, France.
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Chmelova M, Androvic P, Kirdajova D, Tureckova J, Kriska J, Valihrach L, Anderova M, Vargova L. A view of the genetic and proteomic profile of extracellular matrix molecules in aging and stroke. Front Cell Neurosci 2023; 17:1296455. [PMID: 38107409 PMCID: PMC10723838 DOI: 10.3389/fncel.2023.1296455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction Modification of the extracellular matrix (ECM) is one of the major processes in the pathology of brain damage following an ischemic stroke. However, our understanding of how age-related ECM alterations may affect stroke pathophysiology and its outcome is still very limited. Methods We conducted an ECM-targeted re-analysis of our previously obtained RNA-Seq dataset of aging, ischemic stroke and their interactions in young adult (3-month-old) and aged (18-month-old) mice. The permanent middle cerebral artery occlusion (pMCAo) in rodents was used as a model of ischemic stroke. Altogether 56 genes of interest were chosen for this study. Results We identified an increased activation of the genes encoding proteins related to ECM degradation, such as matrix metalloproteinases (MMPs), proteases of a disintegrin and metalloproteinase with the thrombospondin motifs (ADAMTS) family and molecules that regulate their activity, tissue inhibitors of metalloproteinases (TIMPs). Moreover, significant upregulation was also detected in the mRNA of other ECM molecules, such as proteoglycans, syndecans and link proteins. Notably, we identified 8 genes where this upregulation was enhanced in aged mice in comparison with the young ones. Ischemia evoked a significant downregulation in only 6 of our genes of interest, including those encoding proteins associated with the protective function of ECM molecules (e.g., brevican, Hapln4, Sparcl1); downregulation in brevican was more prominent in aged mice. The study was expanded by proteome analysis, where we observed an ischemia-induced overexpression in three proteins, which are associated with neuroinflammation (fibronectin and vitronectin) and neurodegeneration (link protein Hapln2). In fibronectin and Hapln2, this overexpression was more pronounced in aged post-ischemic animals. Conclusion Based on these results, we can conclude that the ratio between the protecting and degrading mechanisms in the aged brain is shifted toward degradation and contributes to the aged tissues' increased sensitivity to ischemic insults. Altogether, our data provide fresh perspectives on the processes underlying ischemic injury in the aging brain and serve as a freely accessible resource for upcoming research.
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Affiliation(s)
- Martina Chmelova
- Department of Neuroscience, Second Faculty of Medicine, Charles University, Prague, Czechia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Peter Androvic
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences – BIOCEV, Vestec, Czechia
| | - Denisa Kirdajova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Tureckova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Jan Kriska
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Lukas Valihrach
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences – BIOCEV, Vestec, Czechia
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Lydia Vargova
- Department of Neuroscience, Second Faculty of Medicine, Charles University, Prague, Czechia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
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50
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El Hayek L, DeVries D, Gogate A, Aiken A, Kaur K, Chahrour MH. Disruption of the autism gene and chromatin regulator KDM5A alters hippocampal cell identity. SCIENCE ADVANCES 2023; 9:eadi0074. [PMID: 37992166 PMCID: PMC10664992 DOI: 10.1126/sciadv.adi0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/25/2023] [Indexed: 11/24/2023]
Abstract
Chromatin regulation plays a pivotal role in establishing and maintaining cellular identity and is one of the top pathways disrupted in autism spectrum disorder (ASD). The hippocampus, composed of distinct cell types, is often affected in patients with ASD. However, the specific hippocampal cell types and their transcriptional programs that are dysregulated in ASD are unknown. Using single-nucleus RNA sequencing, we show that the ASD gene, lysine demethylase 5A (KDM5A), regulates the development of specific subtypes of excitatory and inhibitory neurons. We found that KDM5A is essential for establishing hippocampal cell identity by controlling a differentiation switch early in development. Our findings define a role for the chromatin regulator KDM5A in establishing hippocampal cell identity and contribute to the emerging convergent mechanisms across ASD.
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Affiliation(s)
- Lauretta El Hayek
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Darlene DeVries
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashlesha Gogate
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ariel Aiken
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria H. Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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