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Martín-Zamora FM, Davies BE, Donnellan RD, Guynes K, Martín-Durán JM. Functional genomics in Spiralia. Brief Funct Genomics 2023; 22:487-497. [PMID: 37981859 PMCID: PMC10658182 DOI: 10.1093/bfgp/elad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.
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Affiliation(s)
- Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Asadollahi R, Delvendahl I, Muff R, Tan G, Rodríguez DG, Turan S, Russo M, Oneda B, Joset P, Boonsawat P, Masood R, Mocera M, Ivanovski I, Baumer A, Bachmann-Gagescu R, Schlapbach R, Rehrauer H, Steindl K, Begemann A, Reis A, Winkler J, Winner B, Müller M, Rauch A. Pathogenic SCN2A variants cause early-stage dysfunction in patient-derived neurons. Hum Mol Genet 2023; 32:2192-2204. [PMID: 37010102 PMCID: PMC10281746 DOI: 10.1093/hmg/ddad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/23/2023] [Accepted: 03/19/2023] [Indexed: 04/04/2023] Open
Abstract
Pathogenic heterozygous variants in SCN2A, which encodes the neuronal sodium channel NaV1.2, cause different types of epilepsy or intellectual disability (ID)/autism without seizures. Previous studies using mouse models or heterologous systems suggest that NaV1.2 channel gain-of-function typically causes epilepsy, whereas loss-of-function leads to ID/autism. How altered channel biophysics translate into patient neurons remains unknown. Here, we investigated iPSC-derived early-stage cortical neurons from ID patients harboring diverse pathogenic SCN2A variants [p.(Leu611Valfs*35); p.(Arg937Cys); p.(Trp1716*)] and compared them with neurons from an epileptic encephalopathy (EE) patient [p.(Glu1803Gly)] and controls. ID neurons consistently expressed lower NaV1.2 protein levels. In neurons with the frameshift variant, NaV1.2 mRNA and protein levels were reduced by ~ 50%, suggesting nonsense-mediated decay and haploinsufficiency. In other ID neurons, only protein levels were reduced implying NaV1.2 instability. Electrophysiological analysis revealed decreased sodium current density and impaired action potential (AP) firing in ID neurons, consistent with reduced NaV1.2 levels. In contrast, epilepsy neurons displayed no change in NaV1.2 levels or sodium current density, but impaired sodium channel inactivation. Single-cell transcriptomics identified dysregulation of distinct molecular pathways including inhibition of oxidative phosphorylation in neurons with SCN2A haploinsufficiency and activation of calcium signaling and neurotransmission in epilepsy neurons. Together, our patient iPSC-derived neurons reveal characteristic sodium channel dysfunction consistent with biophysical changes previously observed in heterologous systems. Additionally, our model links the channel dysfunction in ID to reduced NaV1.2 levels and uncovers impaired AP firing in early-stage neurons. The altered molecular pathways may reflect a homeostatic response to NaV1.2 dysfunction and can guide further investigations.
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Affiliation(s)
- R Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
- Faculty of Engineering and Science, University of Greenwich London, Medway Campus, Chatham Maritime ME4 4TB, UK
| | - I Delvendahl
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
| | - R Muff
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - G Tan
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - D G Rodríguez
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - S Turan
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - M Russo
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - B Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - P Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - P Boonsawat
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - R Masood
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - M Mocera
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - I Ivanovski
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - A Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - R Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - R Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - H Rehrauer
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - K Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - A Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
| | - A Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - J Winkler
- Department of Molecular Neurology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
- Center for Rare Diseases Erlangen, University Hospital Erlangen, Erlangen 91054, Germany
| | - B Winner
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
- Center for Rare Diseases Erlangen, University Hospital Erlangen, Erlangen 91054, Germany
| | - M Müller
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
- University of Zurich Clinical Research Priority Program (CRPP) Praeclare – Personalized prenatal and reproductive medicine, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland
| | - A Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich 8952, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich 8057, Switzerland
- University of Zurich Clinical Research Priority Program (CRPP) Praeclare – Personalized prenatal and reproductive medicine, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and Learning, Zurich 8006, Switzerland
- University of Zurich Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare Diseases, Zurich 8006, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich 8057, Switzerland
- University Children's Hospital Zurich, University of Zurich, Zurich 8032, Switzerland
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Stokkermans M, Solis-Escalante T, Cohen MX, Weerdesteyn V. Midfrontal theta dynamics index the monitoring of postural stability. Cereb Cortex 2023; 33:3454-3466. [PMID: 36066445 PMCID: PMC10068289 DOI: 10.1093/cercor/bhac283] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/12/2022] Open
Abstract
Stepping is a common strategy to recover postural stability and maintain upright balance. Postural perturbations have been linked to neuroelectrical markers such as the N1 potential and theta frequency dynamics. Here, we investigated the role of cortical midfrontal theta dynamics of balance monitoring, driven by balance perturbations at different initial standing postures. We recorded electroencephalography, electromyography, and motion tracking of human participants while they stood on a platform that delivered a range of forward and backward whole-body balance perturbations. The participants' postural threat was manipulated prior to the balance perturbation by instructing them to lean forward or backward while keeping their feet-in-place in response to the perturbation. We hypothesized that midfrontal theta dynamics index the engagement of a behavioral monitoring system and, therefore, that perturbation-induced theta power would be modulated by the initial leaning posture and perturbation intensity. Targeted spatial filtering in combination with mixed-effects modeling confirmed our hypothesis and revealed distinct modulations of theta power according to postural threat. Our results provide novel evidence that midfrontal theta dynamics subserve action monitoring of human postural balance. Understanding of cortical mechanisms of balance control is crucial for studying balance impairments related to aging and neurological conditions (e.g. stroke).
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Affiliation(s)
- Mitchel Stokkermans
- Radboud Universitary Medical centre for Medical Neuroscience, Department of Rehabilitation, Reinier Postlaan 4, 6525 GC Nijmegen, The Netherlands
- Donders Institute for Brain cognition and behavior, Department of synchronisation in neural systems Kappitelweg 29,6525 EN Nijmegen, The Netherlands
| | - Teodoro Solis-Escalante
- Radboud Universitary Medical centre for Medical Neuroscience, Department of Rehabilitation, Reinier Postlaan 4, 6525 GC Nijmegen, The Netherlands
| | - Michael X Cohen
- Donders Institute for Brain cognition and behavior, Department of synchronisation in neural systems Kappitelweg 29,6525 EN Nijmegen, The Netherlands
| | - Vivian Weerdesteyn
- Radboud Universitary Medical centre for Medical Neuroscience, Department of Rehabilitation, Reinier Postlaan 4, 6525 GC Nijmegen, The Netherlands
- Sint-Maartenskliniek Research, Hengstdal 3, Ubbergen, 6574 NA Nijmegen, The Netherlands
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5
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Olafson E, Bedford SA, Devenyi GA, Patel R, Tullo S, Park MTM, Parent O, Anagnostou E, Baron-Cohen S, Bullmore ET, Chura LR, Craig MC, Ecker C, Floris DL, Holt RJ, Lenroot R, Lerch JP, Lombardo MV, Murphy DGM, Raznahan A, Ruigrok ANV, Spencer MD, Suckling J, Taylor MJ, Lai MC, Chakravarty MM. Examining the Boundary Sharpness Coefficient as an Index of Cortical Microstructure in Autism Spectrum Disorder. Cereb Cortex 2021; 31:3338-3352. [PMID: 33693614 PMCID: PMC8196259 DOI: 10.1093/cercor/bhab015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 12/06/2020] [Accepted: 01/15/2021] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) is associated with atypical brain development. However, the phenotype of regionally specific increased cortical thickness observed in ASD may be driven by several independent biological processes that influence the gray/white matter boundary, such as synaptic pruning, myelination, or atypical migration. Here, we propose to use the boundary sharpness coefficient (BSC), a proxy for alterations in microstructure at the cortical gray/white matter boundary, to investigate brain differences in individuals with ASD, including factors that may influence ASD-related heterogeneity (age, sex, and intelligence quotient). Using a vertex-based meta-analysis and a large multicenter structural magnetic resonance imaging (MRI) dataset, with a total of 1136 individuals, 415 with ASD (112 female; 303 male), and 721 controls (283 female; 438 male), we observed that individuals with ASD had significantly greater BSC in the bilateral superior temporal gyrus and left inferior frontal gyrus indicating an abrupt transition (high contrast) between white matter and cortical intensities. Individuals with ASD under 18 had significantly greater BSC in the bilateral superior temporal gyrus and right postcentral gyrus; individuals with ASD over 18 had significantly increased BSC in the bilateral precuneus and superior temporal gyrus. Increases were observed in different brain regions in males and females, with larger effect sizes in females. BSC correlated with ADOS-2 Calibrated Severity Score in individuals with ASD in the right medial temporal pole. Importantly, there was a significant spatial overlap between maps of the effect of diagnosis on BSC when compared with cortical thickness. These results invite studies to use BSC as a possible new measure of cortical development in ASD and to further examine the microstructural underpinnings of BSC-related differences and their impact on measures of cortical morphology.
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Affiliation(s)
- Emily Olafson
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal H4H 1R3, Canada
- Department of Neuroscience, Weill Cornell Graduate School of Medical Sciences, New York City, NY 10021, USA
| | - Saashi A Bedford
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal H4H 1R3, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 2B4, Canada
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
| | - Gabriel A Devenyi
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal H3A 2B4, Canada
| | - Raihaan Patel
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal H4H 1R3, Canada
- Department of Biological and Biomedical Engineering, McGill University, Montreal H3A 2B4, Canada
| | - Stephanie Tullo
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal H4H 1R3, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 2B4, Canada
| | - Min Tae M Park
- Department of Psychiatry, Schulich School of Medicine and Dentistry, Western University, London N6A 3K7, ON, Canada
| | - Olivier Parent
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal H4H 1R3, Canada
- Departement de Psychologie, Universite de Montreal, Montreal, QC, Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto M4G 1R8, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Simon Baron-Cohen
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
| | - Edward T Bullmore
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Lindsay R Chura
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
| | - Michael C Craig
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- National Autism Unit, Bethlem Royal Hospital, London BR3 3BX, UK
| | - Christine Ecker
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital of the Goethe University, Frankfurt am Main 60528, Germany
| | - Dorothea L Floris
- Donders Center for Brain, Cognition and Behavior, Radboud University Nijmegen, Nijmegen 6525 HR, The Netherlands
- Department for Cognitive Neuroscience, Radboud University Medical Center Nijmegen, Nijmegen 02.275, The Netherlands
| | - Rosemary J Holt
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
| | - Rhoshel Lenroot
- Department of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jason P Lerch
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford OX3 9DU, UK
| | - Michael V Lombardo
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems, @UniTn, Istituto Italiano di Tecnologia, 38068 Rovereto, Italy
| | - Declan G M Murphy
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, Bethesda, MD 20892-9663, USA
| | - Amber N V Ruigrok
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
| | - Michael D Spencer
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
| | - John Suckling
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Margot J Taylor
- Diagnostic Imaging, The Hospital for Sick Children, Toronto M5G 1X8, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto M5G 1X8, Canada
- Department of Medical Imaging, University of Toronto, Toronto M5G 1X8, Canada
| | | | - Meng-Chuan Lai
- Autism Research Center, Department of Psychiatry, University of Cambridge, Cambridge CB2 8AH, UK
- The Margaret and Wallace McCain Centre for Child, Youth & Family Mental Health and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, Toronto M5T 1R8, Canada
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei 100229, Taiwan
- Department of Psychiatry, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - M Mallar Chakravarty
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal H4H 1R3, Canada
- Integrated Program in Neuroscience, McGill University, Montreal H3A 2B4, Canada
- Department of Psychiatry, McGill University, Montreal H3A 2B4, Canada
- Department of Biological and Biomedical Engineering, McGill University, Montreal H3A 2B4, Canada
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