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Pande S, Majethia P, Nair K, Rao LP, Mascarenhas S, Kaur N, do Rosario MC, Neethukrishna K, Chaurasia A, Hunakunti B, Jadhav N, Xavier S, Kumar J, Bhat V, Bhavani GS, Narayanan DL, Yatheesha BL, Patil SJ, Nampoothiri S, Kamath N, Aroor S, Bhat Y R, Lewis LE, Sharma S, Bajaj S, Sankhyan N, Siddiqui S, Nayak SS, Bielas S, Girisha KM, Shukla A. De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India. Eur J Hum Genet 2024; 32:1291-1298. [PMID: 38114583 PMCID: PMC7616498 DOI: 10.1038/s41431-023-01513-7] [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: 06/29/2023] [Revised: 09/21/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
The contribution of de novo variants as a cause of intellectual disability (ID) is well established in several cohorts reported from the developed world. However, the genetic landscape as well as the appropriate testing strategies for identification of de novo variants of these disorders remain largely unknown in low-and middle-income countries like India. In this study, we delineate the clinical and genotypic spectrum of 54 families (55 individuals) with syndromic ID harboring rare de novo variants. We also emphasize on the effectiveness of singleton exome sequencing as a valuable tool for diagnosing these disorders in resource limited settings. Overall, 46 distinct disorders were identified encompassing 46 genes with 51 single-nucleotide variants and/or indels and two copy-number variants. Pathogenic variants were identified in CREBBP, TSC2, KMT2D, MECP2, IDS, NIPBL, NSD1, RIT1, SOX10, BRWD3, FOXG1, BCL11A, KDM6B, KDM5C, SETD5, QRICH1, DCX, SMARCD1, ASXL1, ASXL3, AKT3, FBN2, TCF12, WASF1, BRAF, SMARCA4, SMARCA2, TUBG1, KMT2A, CTNNB1, DLG4, MEIS2, GATAD2B, FBXW7, ANKRD11, ARID1B, DYNC1H1, HIVEP2, NEXMIF, ZBTB18, SETD1B, DYRK1A, SRCAP, CASK, L1CAM, and KRAS. Twenty-four of these monogenic disorders have not been previously reported in the Indian population. Notably, 39 out of 53 (74%) disease-causing variants are novel. These variants were identified in the genes mainly encoding transcriptional and chromatin regulators, serine threonine kinases, lysosomal enzymes, molecular motors, synaptic proteins, neuronal migration machinery, adhesion molecules, structural proteins and signaling molecules.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Bhagesh Hunakunti
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nalesh Jadhav
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sruthy Xavier
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jeevan Kumar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - B L Yatheesha
- Dheemahi Child Neurology and Development Center, Shivamogga, India
| | - Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran Aroor
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie E Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Neurology Division, Department of Pediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | | | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Shahyan Siddiqui
- Department of Neuro and Vascular Interventional Radiology, Yashoda Hospitals, Secunderabad, Hyderabad, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited, Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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Taylor SR, Kobayashi M, Vilella A, Tiwari D, Zolboot N, Du JX, Spencer KR, Hartzell A, Girgiss C, Abaci YT, Shao Y, De Sanctis C, Bellenchi GC, Darnell RB, Gross C, Zoli M, Berg DK, Lippi G. MicroRNA-218 instructs proper assembly of hippocampal networks. eLife 2023; 12:e82729. [PMID: 37862092 PMCID: PMC10637775 DOI: 10.7554/elife.82729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
The assembly of the mammalian brain is orchestrated by temporally coordinated waves of gene expression. Post-transcriptional regulation by microRNAs (miRNAs) is a key aspect of this program. Indeed, deletion of neuron-enriched miRNAs induces strong developmental phenotypes, and miRNA levels are altered in patients with neurodevelopmental disorders. However, the mechanisms used by miRNAs to instruct brain development remain largely unexplored. Here, we identified miR-218 as a critical regulator of hippocampal assembly. MiR-218 is highly expressed in the hippocampus and enriched in both excitatory principal neurons (PNs) and GABAergic inhibitory interneurons (INs). Early life inhibition of miR-218 results in an adult brain with a predisposition to seizures. Changes in gene expression in the absence of miR-218 suggest that network assembly is impaired. Indeed, we find that miR-218 inhibition results in the disruption of early depolarizing GABAergic signaling, structural defects in dendritic spines, and altered intrinsic membrane excitability. Conditional knockout of Mir218-2 in INs, but not PNs, is sufficient to recapitulate long-term instability. Finally, de-repressing Kif21b and Syt13, two miR-218 targets, phenocopies the effects on early synchronous network activity induced by miR-218 inhibition. Taken together, the data suggest that miR-218 orchestrates formative events in PNs and INs to produce stable networks.
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Affiliation(s)
- Seth R Taylor
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Mariko Kobayashi
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller UniversityNew YorkUnited States
| | - Antonietta Vilella
- Department of Biomedical, Metabolic and Neural Sciences; Center for Neuroscience and Neurotechnology (CfNN), University of Modena and Reggio EmiliaModenaItaly
| | - Durgesh Tiwari
- Division of Neurology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Department of Pediatrics, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Norjin Zolboot
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Jessica X Du
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Kathryn R Spencer
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Andrea Hartzell
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Carol Girgiss
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yusuf T Abaci
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yufeng Shao
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | | | - Gian Carlo Bellenchi
- Institute of Genetics and Biophysics A Buzzati-TraversoNaplesItaly
- IRCCS Fondazione Santa LuciaRomeItaly
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller UniversityNew YorkUnited States
| | - Christina Gross
- Division of Neurology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Department of Pediatrics, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Michele Zoli
- Department of Biomedical, Metabolic and Neural Sciences; Center for Neuroscience and Neurotechnology (CfNN), University of Modena and Reggio EmiliaModenaItaly
| | - Darwin K Berg
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Giordano Lippi
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
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Rivera Alvarez J, Asselin L, Tilly P, Benoit R, Batisse C, Richert L, Batisse J, Morlet B, Levet F, Schwaller N, Mély Y, Ruff M, Reymann AC, Godin JD. The kinesin Kif21b regulates radial migration of cortical projection neurons through a non-canonical function on actin cytoskeleton. Cell Rep 2023; 42:112744. [PMID: 37418324 DOI: 10.1016/j.celrep.2023.112744] [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: 12/13/2022] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/09/2023] Open
Abstract
Completion of neuronal migration is critical for brain development. Kif21b is a plus-end-directed kinesin motor protein that promotes intracellular transport and controls microtubule dynamics in neurons. Here we report a physiological function of Kif21b during radial migration of projection neurons in the mouse developing cortex. In vivo analysis in mouse and live imaging on cultured slices demonstrate that Kif21b regulates the radial glia-guided locomotion of newborn neurons independently of its motility on microtubules. We show that Kif21b directly binds and regulates the actin cytoskeleton both in vitro and in vivo in migratory neurons. We establish that Kif21b-mediated regulation of actin cytoskeleton dynamics influences branching and nucleokinesis during neuronal locomotion. Altogether, our results reveal atypical roles of Kif21b on the actin cytoskeleton during migration of cortical projection neurons.
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Affiliation(s)
- José Rivera Alvarez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Laure Asselin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Peggy Tilly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Roxane Benoit
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Claire Batisse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Ludovic Richert
- Université de Strasbourg, 67000 Strasbourg, France; Laboratoire de Bioimagerie et Pathologies, Centre National de la Recherche Scientifique, UMR 7021, 67404 Illkirch, France
| | - Julien Batisse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Florian Levet
- University of Bordeaux, CNRS, UMR 5297, Interdisciplinary Institute for Neuroscience, IINS, 33000 Bordeaux, France; University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UAR 3420, US 4, 33600 Pessac, France
| | - Noémie Schwaller
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Yves Mély
- Université de Strasbourg, 67000 Strasbourg, France; Laboratoire de Bioimagerie et Pathologies, Centre National de la Recherche Scientifique, UMR 7021, 67404 Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Anne-Cécile Reymann
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Juliette D Godin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC, 67404 Illkirch, France; Centre National de la Recherche Scientifique, CNRS, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, INSERM, U1258, 67404 Illkirch, France; Université de Strasbourg, 67000 Strasbourg, France.
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Ganchala D, Pinto-Benito D, Baides E, Ruiz-Palmero I, Grassi D, Arevalo MA. Kif21B mediates the effect of estradiol on the morphological plasticity of mouse hippocampal neurons. Front Mol Neurosci 2023; 16:1143024. [PMID: 37078090 PMCID: PMC10106616 DOI: 10.3389/fnmol.2023.1143024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/16/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionNeurons are polarized cells, and their ability to change their morphology has a functional implication in the development and plasticity of the nervous system in order to establish new connections. Extracellular factors strongly influence neuronal shape and connectivity. For instance, the developmental actions of estradiol on hippocampal neurons are well characterized, and we have demonstrated in previous studies that Ngn3 mediates these actions. On the other hand, Kif21B regulates microtubule dynamics and carries out retrograde transport of the TrkB/brain-derived neurotrophic factor (BDNF) complex, essential for neuronal development.MethodsIn the present study, we assessed the involvement of kinesin Kif21B in the estradiol-dependent signaling mechanisms to regulate neuritogenesis through cultured mouse hippocampal neurons.ResultsWe show that estradiol treatment increases BDNF expression, and estradiol and BDNF modify neuron morphology through TrkB signaling. Treatment with K252a, a TrkB inhibitor, decreases dendrite branching without affecting axonal length, whereas. Combined with estradiol or BDNF, it blocks their effects on axons but not dendrites. Notably, the downregulation of Kif21B abolishes the actions of estradiol and BDNF in both the axon and dendrites. In addition, Kif21B silencing also decreases Ngn3 expression, and downregulation of Ngn3 blocks the effect of BDNF on neuron morphology.DiscussionThese results suggest that Kif21B is required for the effects of estradiol and BDNF on neuronal morphology, but phosphorylation-mediated activation of TrkB is essential only for axonal growth. Our results show that the Estradiol/BDNF/TrkB/Kif21B/Ngn3 is a new and essential pathway mediating hippocampal neuron development.
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Affiliation(s)
| | - Daniel Pinto-Benito
- Instituto Cajal (IC), CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Isabel Ruiz-Palmero
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Proteómica, Instituto Biosanitario de Granada-IBS, Fundación Para la Investigación Biosanitaria de Andalucía Oriental—Alejandro Otero (FIBAO), Antiguo Hospital Universitario San Cecilio, Unidad de Apoyo a la Investigación (UNAI), Granada, Spain
| | - Daniela Grassi
- Instituto Cajal (IC), CSIC, Madrid, Spain
- Department of Anatomy, Histology and Neuroscience, Autonoma University of Madrid, Madrid, Spain
| | - Maria Angeles Arevalo
- Instituto Cajal (IC), CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Maria Angeles Arevalo,
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