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Akula SK, Chen AY, Neil JE, Shao DD, Mo A, Hylton NK, DiTroia S, Ganesh VS, Smith RS, O’Kane K, Yeh RC, Marciano JH, Kirkham S, Kenny CJ, Song JHT, Al Saffar M, Millan F, Harris DJ, Murphy AV, Klemp KC, Braddock SR, Brand H, Wong I, Talkowski ME, O’Donnell-Luria A, Lai A, Hill RS, Mochida GH, Doan RN, Barkovich AJ, Yang E, Amrom D, Andermann E, Poduri A, Walsh CA. Exome Sequencing and the Identification of New Genes and Shared Mechanisms in Polymicrogyria. JAMA Neurol 2023; 80:980-988. [PMID: 37486637 PMCID: PMC10366952 DOI: 10.1001/jamaneurol.2023.2363] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/27/2022] [Accepted: 03/23/2023] [Indexed: 07/25/2023]
Abstract
Importance Polymicrogyria is the most commonly diagnosed cortical malformation and is associated with neurodevelopmental sequelae including epilepsy, motor abnormalities, and cognitive deficits. Polymicrogyria frequently co-occurs with other brain malformations or as part of syndromic diseases. Past studies of polymicrogyria have defined heterogeneous genetic and nongenetic causes but have explained only a small fraction of cases. Objective To survey germline genetic causes of polymicrogyria in a large cohort and to consider novel polymicrogyria gene associations. Design, Setting, and Participants This genetic association study analyzed panel sequencing and exome sequencing of accrued DNA samples from a retrospective cohort of families with members with polymicrogyria. Samples were accrued over more than 20 years (1994 to 2020), and sequencing occurred in 2 stages: panel sequencing (June 2015 to January 2016) and whole-exome sequencing (September 2019 to March 2020). Individuals seen at multiple clinical sites for neurological complaints found to have polymicrogyria on neuroimaging, then referred to the research team by evaluating clinicians, were included in the study. Targeted next-generation sequencing and/or exome sequencing were performed on probands (and available parents and siblings) from 284 families with individuals who had isolated polymicrogyria or polymicrogyria as part of a clinical syndrome and no genetic diagnosis at time of referral from clinic, with sequencing from 275 families passing quality control. Main Outcomes and Measures The number of families in whom genetic sequencing yielded a molecular diagnosis that explained the polymicrogyria in the family. Secondarily, the relative frequency of different genetic causes of polymicrogyria and whether specific genetic causes were associated with co-occurring head size changes were also analyzed. Results In 32.7% (90 of 275) of polymicrogyria-affected families, genetic variants were identified that provided satisfactory molecular explanations. Known genes most frequently implicated by polymicrogyria-associated variants in this cohort were PIK3R2, TUBB2B, COL4A1, and SCN3A. Six candidate novel polymicrogyria genes were identified or confirmed: de novo missense variants in PANX1, QRICH1, and SCN2A and compound heterozygous variants in TMEM161B, KIF26A, and MAN2C1, each with consistent genotype-phenotype relationships in multiple families. Conclusions and Relevance This study's findings reveal a higher than previously recognized rate of identifiable genetic causes, specifically of channelopathies, in individuals with polymicrogyria and support the utility of exome sequencing for families affected with polymicrogyria.
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Affiliation(s)
- Shyam K. Akula
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, Massachusetts
| | - Allen Y. Chen
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Division of Rheumatology, Hospital for Special Surgery, New York, New York
| | - Jennifer E. Neil
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Diane D. Shao
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Alisa Mo
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Norma K. Hylton
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, Massachusetts
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Vijay S. Ganesh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Richard S. Smith
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Katherine O’Kane
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Rebecca C. Yeh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Jack H. Marciano
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Samantha Kirkham
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Connor J. Kenny
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Janet H. T. Song
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Muna Al Saffar
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Department of Genetics and Genomics, United Arab Emirates University, United Arab Emirates
| | | | - David J. Harris
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Andrea V. Murphy
- Division of Medical Genetics, Our Lady of the Lake Health System, Baton Rouge, Louisiana
| | - Kara C. Klemp
- Division of Medical Genetics, Department of Pediatrics Saint Louis University School of Medicine, St Louis, Missouri
| | - Stephen R. Braddock
- Division of Medical Genetics, Department of Pediatrics Saint Louis University School of Medicine, St Louis, Missouri
| | - Harrison Brand
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Isaac Wong
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Michael E. Talkowski
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Abbe Lai
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
| | - Robert Sean Hill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Ganeshwaran H. Mochida
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
| | - Ryan N. Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
| | - A. James Barkovich
- Benioff Children’s Hospital, Departments of Radiology, Pediatrics, Neurology, and Neurological Surgery, University of California, San Francisco, San Francisco
| | - Edward Yang
- Department of Radiology, Boston Children’s Hospital, Boston, Massachusetts
| | - Dina Amrom
- Neurogenetics Unit, Montreal Neurological Hospital and Institute, Montreal, Quebec, Canada
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Neurology, Queen Fabiola Children’s University Hospital, Brussels, Belgium
- Pediatric Neurology Unit, Centre Hospitalier de Luxembourg, Grand-Duchy of Luxembourg
| | - Eva Andermann
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada
- Pediatric Neurology Unit, Centre Hospitalier de Luxembourg, Grand-Duchy of Luxembourg
- Epilepsy Research Group, Montreal Neurological Hospital and Institute, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Annapurna Poduri
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, and Allen Discovery Center for Human Brain Evolution, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts
- Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, Massachusetts
- Program in Medical and Population Genetics, Center for Genomic Medicine, Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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2
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Akula SK, Marciano JH, Lim Y, Exposito-Alonso D, Hylton NK, Hwang GH, Neil JE, Dominado N, Bunton-Stasyshyn RK, Song JHT, Talukdar M, Schmid A, Teboul L, Mo A, Shin T, Finander B, Beck SG, Yeh RC, Otani A, Qian X, DeGennaro EM, Alkuraya FS, Maddirevula S, Cascino GD, Giannini C, Burrage LC, Rosenfield JA, Ketkar S, Clark GD, Bacino C, Lewis RA, Segal RA, Bazan JF, Smith KA, Golden JA, Cho G, Walsh CA. TMEM161B regulates cerebral cortical gyration, Sonic Hedgehog signaling, and ciliary structure in the developing central nervous system. Proc Natl Acad Sci U S A 2023; 120:e2209964120. [PMID: 36669111 PMCID: PMC9942790 DOI: 10.1073/pnas.2209964120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 12/14/2022] [Indexed: 01/22/2023] Open
Abstract
Sonic hedgehog signaling regulates processes of embryonic development across multiple tissues, yet factors regulating context-specific Shh signaling remain poorly understood. Exome sequencing of families with polymicrogyria (disordered cortical folding) revealed multiple individuals with biallelic deleterious variants in TMEM161B, which encodes a multi-pass transmembrane protein of unknown function. Tmem161b null mice demonstrated holoprosencephaly, craniofacial midline defects, eye defects, and spinal cord patterning changes consistent with impaired Shh signaling, but were without limb defects, suggesting a CNS-specific role of Tmem161b. Tmem161b depletion impaired the response to Smoothened activation in vitro and disrupted cortical histogenesis in vivo in both mouse and ferret models, including leading to abnormal gyration in the ferret model. Tmem161b localizes non-exclusively to the primary cilium, and scanning electron microscopy revealed shortened, dysmorphic, and ballooned ventricular zone cilia in the Tmem161b null mouse, suggesting that the Shh-related phenotypes may reflect ciliary dysfunction. Our data identify TMEM161B as a regulator of cerebral cortical gyration, as involved in primary ciliary structure, as a regulator of Shh signaling, and further implicate Shh signaling in human gyral development.
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Affiliation(s)
- Shyam K. Akula
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Harvard-Massachusetts Institute of Technology MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Jack H. Marciano
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Youngshin Lim
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA90048
| | - David Exposito-Alonso
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Norma K. Hylton
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Harvard-Massachusetts Institute of Technology MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Grace H. Hwang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA02115
- Department of Neurobiology, Harvard Medical School, Boston, MA02115
| | - Jennifer E. Neil
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
| | - Nicole Dominado
- Department of Anatomy & Physiology, The University of Melbourne, Melbourne, VIC3010, Australia
| | | | - Janet H. T. Song
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Maya Talukdar
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Harvard-Massachusetts Institute of Technology MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Aloisia Schmid
- Department of Physics/Electron Microscopy Core, Northeastern University, Boston, MA02115
| | - Lydia Teboul
- Mary Lyon Centre, United Kingdom Medical Research Council Harwell, Didcot, Oxfordshire,OX11 0RD, UK
| | - Alisa Mo
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
| | - Taehwan Shin
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Benjamin Finander
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Samantha G. Beck
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
| | - Rebecca C. Yeh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
| | - Aoi Otani
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
| | - Xuyu Qian
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
| | - Ellen M. DeGennaro
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, 11564 Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, 11564 Riyadh, Saudi Arabia
| | | | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN55905
| | | | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Departments of Pediatrics, Baylor College of Medicine, Houston, TX77030
- Neurology, Baylor College of Medicine, Houston, TX77030
- Neuroscience, Baylor College of Medicine, Houston, TX77030
| | - Jill A. Rosenfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
| | - Gary D. Clark
- Departments of Pediatrics, Baylor College of Medicine, Houston, TX77030
- Neurology, Baylor College of Medicine, Houston, TX77030
- Neuroscience, Baylor College of Medicine, Houston, TX77030
| | - Carlos Bacino
- Departments of Pediatrics, Baylor College of Medicine, Houston, TX77030
- Neurology, Baylor College of Medicine, Houston, TX77030
- Neuroscience, Baylor College of Medicine, Houston, TX77030
| | - Richard A. Lewis
- Departments of Pediatrics, Baylor College of Medicine, Houston, TX77030
- Neurology, Baylor College of Medicine, Houston, TX77030
- Neuroscience, Baylor College of Medicine, Houston, TX77030
| | - Rosalind A. Segal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA02115
- Department of Neurobiology, Harvard Medical School, Boston, MA02115
| | - J. Fernando Bazan
- Unit for Structural Biology, Vlaams Instituut voor Biotechnologie-UGent Center for Inflammation Research, 9052Ghent, Belgium
| | - Kelly A. Smith
- Department of Anatomy & Physiology, The University of Melbourne, Melbourne, VIC3010, Australia
| | - Jeffrey A. Golden
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA90048
| | - Ginam Cho
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA90048
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
- Harvard-Massachusetts Institute of Technology MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Howard Hughes Medical Institute, Boston Children’s Hospital Boston, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Neurology, Harvard Medical School, Boston, MA02115
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3
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Qian X, DeGennaro EM, Talukdar M, Akula SK, Lai A, Shao DD, Gonzalez D, Marciano JH, Smith RS, Hylton NK, Yang E, Bazan JF, Barrett L, Yeh RC, Hill RS, Beck SG, Otani A, Angad J, Mitani T, Posey JE, Pehlivan D, Calame D, Aydin H, Yesilbas O, Parks KC, Argilli E, England E, Im K, Taranath A, Scott HS, Barnett CP, Arts P, Sherr EH, Lupski JR, Walsh CA. Loss of non-motor kinesin KIF26A causes congenital brain malformations via dysregulated neuronal migration and axonal growth as well as apoptosis. Dev Cell 2022; 57:2381-2396.e13. [PMID: 36228617 PMCID: PMC10585591 DOI: 10.1016/j.devcel.2022.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/06/2021] [Revised: 06/13/2022] [Accepted: 09/20/2022] [Indexed: 01/16/2023]
Abstract
Kinesins are canonical molecular motors but can also function as modulators of intracellular signaling. KIF26A, an unconventional kinesin that lacks motor activity, inhibits growth-factor-receptor-bound protein 2 (GRB2)- and focal adhesion kinase (FAK)-dependent signal transduction, but its functions in the brain have not been characterized. We report a patient cohort with biallelic loss-of-function variants in KIF26A, exhibiting a spectrum of congenital brain malformations. In the developing brain, KIF26A is preferentially expressed during early- and mid-gestation in excitatory neurons. Combining mice and human iPSC-derived organoid models, we discovered that loss of KIF26A causes excitatory neuron-specific defects in radial migration, localization, dendritic and axonal growth, and apoptosis, offering a convincing explanation of the disease etiology in patients. Single-cell RNA sequencing in KIF26A knockout organoids revealed transcriptional changes in MAPK, MYC, and E2F pathways. Our findings illustrate the pathogenesis of KIF26A loss-of-function variants and identify the surprising versatility of this non-motor kinesin.
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Affiliation(s)
- Xuyu Qian
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen M DeGennaro
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maya Talukdar
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Shyam K Akula
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard, MIT MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Abbe Lai
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Diane D Shao
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dilenny Gonzalez
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jack H Marciano
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Richard S Smith
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Norma K Hylton
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Harvard, MIT MD/PhD Program, Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Edward Yang
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Radiology, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Lee Barrett
- Department of Neurobiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca C Yeh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha G Beck
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aoi Otani
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jolly Angad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey
| | - Osman Yesilbas
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon 61080, Turkey
| | - Kendall C Parks
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eleina England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiho Im
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ajay Taranath
- Department of Medical Imaging, South Australia Medical Imaging, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia; Australian Genomics, Parkville, VIC, Australia
| | - Christopher P Barnett
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Pediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA; Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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4
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Patnaik D, Pao PC, Zhao WN, Silva MC, Hylton NK, Chindavong PS, Pan L, Tsai LH, Haggarty SJ. Exifone Is a Potent HDAC1 Activator with Neuroprotective Activity in Human Neuronal Models of Neurodegeneration. ACS Chem Neurosci 2021; 12:271-284. [PMID: 33417763 DOI: 10.1021/acschemneuro.0c00308] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genomic instability caused by a deficiency in the DNA damage response and repair has been linked to age-related cognitive decline and neurodegenerative diseases. Preventing genomic instability that ultimately leads to neuronal death may provide a broadly effective strategy to protect against multiple potential genotoxic stressors. Recently, the zinc-dependent class I histone deacetylase (HDAC1) has been identified as a critical factor for protecting neurons from deleterious effects of DNA damage in Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). Translating these observations to a novel neuroprotective therapy for AD, ALS, and FTD may be advanced by the identification of small molecules capable of increasing the deacetylase activity of HDAC1 selectively over other structurally similar HDACs. Here, we demonstrate that exifone, a drug previously shown to be effective in treating cognitive deficits associated with AD and Parkinson's disease, the molecular mechanism of which has remained poorly understood, potently activates the deacetylase activity of HDAC1. We show that exifone acts as a mixed, nonessential activator of HDAC1 that is capable of binding to both free and substrate-bound enzyme, resulting in an increased relative maximal rate of HDAC1-catalyzed deacetylation. Exifone can directly bind to HDAC1 based upon biolayer interferometry assays with kinetic and selectivity profiling, suggesting that HDAC1 is preferentially targeted compared to other class I HDACs and the kinase CDK5, which have also been implicated in neurodegeneration. Consistent with a mechanism of deacetylase activation intracellularly, the treatment of human induced pluripotent stem cell (iPSC)-derived neuronal cells resulted in globally decreased histone acetylation. Moreover, exifone treatment was neuroprotective in a tauopathy patient iPSC-derived neuronal model subject to oxidative stress. Taken together, these findings reveal exifone as a potent activator of HDAC1-mediated deacetylation, thereby offering a lead for novel therapeutic development aiming to protect genomic integrity in the context of neurodegeneration and aging.
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Affiliation(s)
- Debasis Patnaik
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ping-Chieh Pao
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - M. Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Norma K. Hylton
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Peter S. Chindavong
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ling Pan
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Departments of Psychiatry & Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02114, United States
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5
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Zhao WN, Hylton NK, Wang J, Chindavong PS, Alural B, Kurtser I, Subramanian A, Mazitschek R, Perlis RH, Haggarty SJ. Activation of WNT and CREB signaling pathways in human neuronal cells in response to the Omega-3 fatty acid docosahexaenoic acid (DHA). Mol Cell Neurosci 2019; 99:103386. [PMID: 31202891 PMCID: PMC7001743 DOI: 10.1016/j.mcn.2019.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 01/16/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
A subset of individuals with major depressive disorder (MDD) elects treatment with complementary and alternative medicines (CAMs), including the omega-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Previous studies in rodents suggest that DHA modulates neurodevelopmental processes, including adult neurogenesis and neuroplasticity, but the molecular and cellular mechanisms of DHA's potential therapeutic effect in the context of human neurobiology have not been well established. Here we sought to address this knowledge gap by investigating the effects of DHA using human iPSC-derived neural progenitor cells (NPCs) and post-mitotic neurons using pathway-selective reporter genes, multiplexed mRNA expression profiling, and a panel of metabolism-based viability assays. Finally, real-time, live-cell imaging was employed to monitor neurite outgrowth upon DHA treatment. Overall, these studies showed that DHA treatment (0-50 μM) significantly upregulated both WNT and CREB signaling pathways in human neuronal cells in a dose-dependent manner with 2- to 3-fold increases in pathway activation. Additionally, we observed that DHA treatment enhanced survival of iPSC-derived NPCs and differentiation of post-mitotic neurons with live-cell imaging, revealing increased neurite outgrowth with DHA treatment within 24 h. Taken together, this study provides evidence that DHA treatment activates critical pathways regulating neuroplasticity, which may contribute to enhanced neuronal cell viability and neuronal connectivity. The extent to which these pathways represent molecular mechanisms underlying the potential beneficial effects of omega-3 fatty acids in MDD and other brain disorders merits further investigation.
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Affiliation(s)
- Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America
| | - Norma K Hylton
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America
| | - Jennifer Wang
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America; Center for Quantitative Health, Center for Genomic Medicine, Division of Clinical Research, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America
| | - Peter S Chindavong
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America
| | - Begum Alural
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America; Department of Neuroscience, Institute of Health Sciences, Dokuz Eylul University, Izmir 35210, Turkey
| | - Iren Kurtser
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America
| | - Aravind Subramanian
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States of America
| | - Ralph Mazitschek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States of America; Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America
| | - Roy H Perlis
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America; Center for Quantitative Health, Center for Genomic Medicine, Division of Clinical Research, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America.
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States of America; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America.
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