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Xiong GJ, Sheng ZH. Presynaptic perspective: Axonal transport defects in neurodevelopmental disorders. J Cell Biol 2024; 223:e202401145. [PMID: 38568173 PMCID: PMC10988239 DOI: 10.1083/jcb.202401145] [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: 01/27/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Disruption of synapse assembly and maturation leads to a broad spectrum of neurodevelopmental disorders. Presynaptic proteins are largely synthesized in the soma, where they are packaged into precursor vesicles and transported into distal axons to ensure precise assembly and maintenance of presynapses. Due to their morphological features, neurons face challenges in the delivery of presynaptic cargos to nascent boutons. Thus, targeted axonal transport is vital to build functional synapses. A growing number of mutations in genes encoding the transport machinery have been linked to neurodevelopmental disorders. Emerging lines of evidence have started to uncover presynaptic mechanisms underlying axonal transport defects, thus broadening the view of neurodevelopmental disorders beyond postsynaptic mechanisms. In this review, we discuss presynaptic perspectives of neurodevelopmental disorders by focusing on impaired axonal transport and disturbed assembly and maintenance of presynapses. We also discuss potential strategies for restoring axonal transport as an early therapeutic intervention.
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Affiliation(s)
- Gui-Jing Xiong
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Zu-Hang Sheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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2
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Cabet S, Putoux A, Lesca G, Lesage A, Massoud M, Guibaud L. Prenatal diagnosis of microcephaly with simplified gyral pattern: series of eight cases. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:271-275. [PMID: 37551048 DOI: 10.1002/uog.27450] [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: 05/15/2023] [Revised: 07/05/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Microcephaly with simplified gyral pattern (MSG) is an intrinsic genetic central nervous system disorder, characterized by microcephaly (a reduction of brain volume) and a simplified gyral pattern (a reduced number of gyri and shallow sulci associated with normal cortical thickness and neuroanatomical architecture), related to a reduced number of neuronal progenitors in the germinal matrix. We report the first prenatal series of MSG and define the prenatal imaging pattern, which should inform diagnosis and guide prenatal counseling in cases of fetal microcephaly. In this single-center retrospective study of fetuses with MSG, we assessed features on ultrasound and magnetic resonance imaging (MRI), as well as genetic and neuropathological/postnatal data. We included eight patients who had been referred following observation of microcephaly. Ultrasound examination confirmed microcephaly, with a mean growth delay in head circumference of 3.4 weeks, associated with both a lack of gyration and a lack of opercularization of the Sylvian fissure and without any extracephalic anomaly. Fetal brain MRI confirmed lack of gyration with normal cortical thickness and normal intensity of the white matter in all cases. These MRI features led to exclusion of migration/corticogenesis disorders (lissencephaly/polymicrogyria), instead suggesting MSG. The posterior fossa was normal in seven of the eight cases. The corpus callosum was thin in four cases, hypoplastic in two and dysgenetic in two. In four cases, the pregnancy was terminated. The diagnosis of MSG was confirmed from neuropathological and postnatal MRI data. MSG was associated with a genetic diagnosis of RTTN (n = 1) and ASPM (n = 2) biallelic variants in three of the six cases in which genetic work-up was performed. Mild or moderate intellectual deficit with speech delay was present in the three surviving children who were at least 5 years of age at their last examination, without seizures. In conclusion, in the presence of isolated fetal microcephaly with lack of gyration on ultrasound, fetal cerebral MRI is key to diagnosing MSG, which, in the majority of cases, affects the supratentorial space exclusively, and to ruling out other cortical malformations that show a similar sonographic pattern. In addition to imaging, genetic assessment may guide prenatal counseling, since the prenatal prognosis of MSG is different from that of both diffuse polymicrogyria and lissencephaly. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- S Cabet
- Pediatric and Fetal Imaging Department, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France
- Institut NeuroMyoGène, CNRS UMR5292, INSERM U1028, Claude Bernard Lyon 1 University, Lyon, France
- Multidisciplinary Center for Prenatal Diagnosis, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France
| | - A Putoux
- Multidisciplinary Center for Prenatal Diagnosis, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France
- Department of Genetics, Groupement Hospitalier Est, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France
| | - G Lesca
- Institut NeuroMyoGène, CNRS UMR5292, INSERM U1028, Claude Bernard Lyon 1 University, Lyon, France
- Department of Genetics, Groupement Hospitalier Est, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France
| | - A Lesage
- Department of Medical Imaging, CHU Sainte-Justine, Montréal, QC, Canada
| | - M Massoud
- Department of Gynecology and Obstetrics, Multidisciplinary Center for Prenatal Diagnosis, CHLS, Hospices Civils de Lyon, Lyon, France
| | - L Guibaud
- Pediatric and Fetal Imaging Department, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France
- Multidisciplinary Center for Prenatal Diagnosis, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Claude Bernard Lyon 1 University, Lyon, France
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3
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Tsai MH, Ke HC, Lin WC, Nian FS, Huang CW, Cheng HY, Hsu CS, Granata T, Chang CH, Castellotti B, Lin SY, Doniselli FM, Lu CJ, Franceschetti S, Ragona F, Hou PS, Canafoglia L, Tung CY, Lee MH, Wang WJ, Tsai JW. Novel lissencephaly-associated NDEL1 variant reveals distinct roles of NDE1 and NDEL1 in nucleokinesis and human cortical malformations. Acta Neuropathol 2024; 147:13. [PMID: 38194050 PMCID: PMC10776482 DOI: 10.1007/s00401-023-02665-y] [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: 10/23/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024]
Abstract
The development of the cerebral cortex involves a series of dynamic events, including cell proliferation and migration, which rely on the motor protein dynein and its regulators NDE1 and NDEL1. While the loss of function in NDE1 leads to microcephaly-related malformations of cortical development (MCDs), NDEL1 variants have not been detected in MCD patients. Here, we identified two patients with pachygyria, with or without subcortical band heterotopia (SBH), carrying the same de novo somatic mosaic NDEL1 variant, p.Arg105Pro (p.R105P). Through single-cell RNA sequencing and spatial transcriptomic analysis, we observed complementary expression of Nde1/NDE1 and Ndel1/NDEL1 in neural progenitors and post-mitotic neurons, respectively. Ndel1 knockdown by in utero electroporation resulted in impaired neuronal migration, a phenotype that could not be rescued by p.R105P. Remarkably, p.R105P expression alone strongly disrupted neuronal migration, increased the length of the leading process, and impaired nucleus-centrosome coupling, suggesting a failure in nucleokinesis. Mechanistically, p.R105P disrupted NDEL1 binding to the dynein regulator LIS1. This study identifies the first lissencephaly-associated NDEL1 variant and sheds light on the distinct roles of NDE1 and NDEL1 in nucleokinesis and MCD pathogenesis.
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Affiliation(s)
- Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hao-Chen Ke
- Institute of Brain Science, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Medical Education, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Wan-Cian Lin
- Institute of Brain Science, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Faculty of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Fang-Shin Nian
- Institute of Brain Science, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-Wei Huang
- Institute of Brain Science, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Advanced Therapeutics Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Haw-Yuan Cheng
- Institute of Brain Science, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chi-Sin Hsu
- Genomics Center for Clinical and Biotechnological Applications, Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tiziana Granata
- Department of Paediatric Neuroscience, European Reference Network EPIcare, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chien-Hui Chang
- Institute of Brain Science, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Barbara Castellotti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Shin-Yi Lin
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Fabio M Doniselli
- Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cheng-Ju Lu
- Faculty of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Silvana Franceschetti
- Integrated Diagnostics for Epilepsy, Department of Diagnostic and Technology, European Reference Network EPIcare, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesca Ragona
- Department of Paediatric Neuroscience, European Reference Network EPIcare, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Pei-Shan Hou
- Institute of Anatomy and Cell Biology, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Laura Canafoglia
- Integrated Diagnostics for Epilepsy, Department of Diagnostic and Technology, European Reference Network EPIcare, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chien-Yi Tung
- Advanced Therapeutics Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Mei-Hsuan Lee
- Institute of Clinical Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Advanced Therapeutics Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Won-Jing Wang
- Advanced Therapeutics Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Biochemistry and Molecule Biology, College of Life Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jin-Wu Tsai
- Institute of Brain Science, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Advanced Therapeutics Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.
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Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024; 16:5. [PMID: 38185688 PMCID: PMC10773105 DOI: 10.1186/s13073-023-01265-5] [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: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described. METHODS Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank. RESULTS We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS. CONCLUSIONS Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
| | - Maarja Jõeloo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland
| | - Nicolò Tesio
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Sven Ojavee
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Charlie J Clark
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
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5
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Perrottelli A, Marzocchi FF, Caporusso E, Giordano GM, Giuliani L, Melillo A, Pezzella P, Bucci P, Mucci A, Galderisi S. Advances in the understanding of the pathophysiology of schizophrenia and bipolar disorder through induced pluripotent stem cell models. J Psychiatry Neurosci 2024; 49:E109-E125. [PMID: 38490647 PMCID: PMC10950363 DOI: 10.1503/jpn.230112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 08/04/2023] [Accepted: 01/08/2024] [Indexed: 03/17/2024] Open
Abstract
The pathophysiology of schizophrenia and bipolar disorder involves a complex interaction between genetic and environmental factors that begins in the early stages of neurodevelopment. Recent advancements in the field of induced pluripotent stem cells (iPSCs) offer a promising tool for understanding the neurobiological alterations involved in these disorders and, potentially, for developing new treatment options. In this review, we summarize the results of iPSC-based research on schizophrenia and bipolar disorder, showing disturbances in neurodevelopmental processes, imbalance in glutamatergic-GABAergic transmission and neuromorphological alterations. The limitations of the reviewed literature are also highlighted, particularly the methodological heterogeneity of the studies, the limited number of studies developing iPSC models of both diseases simultaneously, and the lack of in-depth clinical characterization of the included samples. Further studies are needed to advance knowledge on the common and disease-specific pathophysiological features of schizophrenia and bipolar disorder and to promote the development of new treatment options.
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Affiliation(s)
| | | | | | | | - Luigi Giuliani
- From the University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Antonio Melillo
- From the University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Paola Bucci
- From the University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Armida Mucci
- From the University of Campania "Luigi Vanvitelli", Naples, Italy
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6
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Okada K, Iyer BR, Lammers LG, Gutierrez PA, Li W, Markus SM, McKenney RJ. Conserved roles for the dynein intermediate chain and Ndel1 in assembly and activation of dynein. Nat Commun 2023; 14:5833. [PMID: 37730751 PMCID: PMC10511499 DOI: 10.1038/s41467-023-41466-5] [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: 03/20/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023] Open
Abstract
Processive transport by the microtubule motor cytoplasmic dynein requires the regulated assembly of a dynein-dynactin-adapter complex. Interactions between dynein and dynactin were initially ascribed to the dynein intermediate chain N-terminus and the dynactin subunit p150Glued. However, recent cryo-EM structures have not resolved this interaction, questioning its importance. The intermediate chain also interacts with Nde1/Ndel1, which compete with p150Glued for binding. We reveal that the intermediate chain N-terminus is a critical evolutionarily conserved hub that interacts with dynactin and Ndel1, the latter of which recruits LIS1 to drive complex assembly. In additon to revealing that the intermediate chain N-terminus is likely bound to p150Glued in active transport complexes, our data support a model whereby Ndel1-LIS1 must dissociate prior to LIS1 being handed off to dynein in temporally discrete steps. Our work reveals previously unknown steps in the dynein activation pathway, and provide insight into the integrated activities of LIS1/Ndel1 and dynactin/cargo-adapters.
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Affiliation(s)
- Kyoko Okada
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Bharat R Iyer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lindsay G Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Pedro A Gutierrez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, 95616, USA
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Wenzhe Li
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Steven M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Richard J McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, 95616, USA.
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7
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Dalton SE, Workalemahu T, Allshouse AA, Page JM, Reddy UM, Saade GR, Pinar H, Goldenberg RL, Dudley DJ, Silver RM. Copy number variants and fetal growth in stillbirths. Am J Obstet Gynecol 2023; 228:579.e1-579.e11. [PMID: 36356697 PMCID: PMC10149588 DOI: 10.1016/j.ajog.2022.11.1274] [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: 04/27/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Fetal growth abnormalities are associated with a higher incidence of stillbirth, with small and large for gestational age infants incurring a 3 to 4- and 2 to 3-fold increased risk, respectively. Although clinical risk factors such as diabetes, hypertension, and placental insufficiency have been associated with fetal growth aberrations and stillbirth, the role of underlying genetic etiologies remains uncertain. OBJECTIVE This study aimed to assess the relationship between abnormal copy number variants and fetal growth abnormalities in stillbirths using chromosomal microarray. STUDY DESIGN A secondary analysis utilizing a cohort study design of stillbirths from the Stillbirth Collaborative Research Network was performed. Exposure was defined as abnormal copy number variants including aneuploidies, pathogenic copy number variants, and variants of unknown clinical significance. The outcomes were small for gestational age and large for gestational age stillbirths, defined as a birthweight <10th percentile and greater than the 90th percentile for gestational age, respectively. RESULTS Among 393 stillbirths with chromosomal microarray and birthweight data, 16% had abnormal copy number variants. The small for gestational age outcome was more common among those with abnormal copy number variants than those with a normal microarray (29.5% vs 16.5%; P=.038). This finding was consistent after adjusting for clinically important variables. In the final model, only abnormal copy number variants and maternal age remained significantly associated with small for gestational age stillbirths, with an adjusted odds ratio of 2.22 (95% confidence interval, 1.12-4.18). Although large for gestational age stillbirths were more likely to have an abnormal microarray: 6.2% vs 3.3% (P=.275), with an odds ratio of 2.35 (95% confidence interval, 0.70-7.90), this finding did not reach statistical significance. CONCLUSION Genetic abnormalities are more common in the setting of small for gestational age stillborn fetuses. Abnormal copy number variants not detectable by traditional karyotype make up approximately 50% of the genetic abnormalities in this population.
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Affiliation(s)
- Susan E Dalton
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT
| | | | | | | | | | - George R Saade
- University of Texas Medical Branch at Galveston, Galveston, TX
| | - Halit Pinar
- Brown University School of Medicine, Providence, RI
| | | | | | - Robert M Silver
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT.
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8
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Okada K, Iyer BR, Lammers LG, Gutierrez P, Li W, Markus SM, McKenney RJ. Conserved Roles for the Dynein Intermediate Chain and Ndel1 in Assembly and Activation of Dynein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523097. [PMID: 36711700 PMCID: PMC9882231 DOI: 10.1101/2023.01.13.523097] [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: 01/15/2023]
Abstract
Cytoplasmic dynein, the primary retrograde microtubule transport motor within cells, must be activated for processive motility through the regulated assembly of a dynein-dynactin-adapter (DDA) complex. The interaction between dynein and dynactin was initially ascribed to the N-terminus of the dynein intermediate chain (IC) and a coiled-coil of the dynactin subunit p150 Glued . However, cryo-EM structures of DDA complexes have not resolve these regions of the IC and p150 Glued , raising questions about the importance of this interaction. The IC N-terminus (ICN) also interacts with the dynein regulators Nde1/Ndel1, which compete with p150 Glued for binding to ICN. Using a combination of approaches, we reveal that the ICN plays critical, evolutionarily conserved roles in DDA assembly by interacting with dynactin and Ndel1, the latter of which recruits the DDA assembly factor LIS1 to the dynein complex. In contrast to prior models, we find that LIS1 cannot simultaneously bind to Ndel1 and dynein, indicating that LIS1 must be handed off from Ndel1 to dynein in temporally discrete steps. Whereas exogenous Ndel1 or p150 Glued disrupts DDA complex assembly in vitro , neither perturbs preassembled DDA complexes, indicating that the IC is stably bound to p150 Glued within activated DDA complexes. Our study reveals previously unknown regulatory steps in the dynein activation pathway, and provides a more complete model for how the activities of LIS1/Ndel1 and dynactin/cargo-adapters are integrated to regulate dynein motor activity.
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Affiliation(s)
- Kyoko Okada
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Bharat R. Iyer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Lindsay G. Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Pedro Gutierrez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Wenzhe Li
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Steven M. Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Richard J. McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
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9
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Primary Cilia Influence Progenitor Function during Cortical Development. Cells 2022; 11:cells11182895. [PMID: 36139475 PMCID: PMC9496791 DOI: 10.3390/cells11182895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Corticogenesis is an intricate process controlled temporally and spatially by many intrinsic and extrinsic factors. Alterations during this important process can lead to severe cortical malformations. Apical neuronal progenitors are essential cells able to self-amplify and also generate basal progenitors and/or neurons. Apical radial glia (aRG) are neuronal progenitors with a unique morphology. They have a long basal process acting as a support for neuronal migration to the cortical plate and a short apical process directed towards the ventricle from which protrudes a primary cilium. This antenna-like structure allows aRG to sense cues from the embryonic cerebrospinal fluid (eCSF) helping to maintain cell shape and to influence several key functions of aRG such as proliferation and differentiation. Centrosomes, major microtubule organising centres, are crucial for cilia formation. In this review, we focus on how primary cilia influence aRG function during cortical development and pathologies which may arise due to defects in this structure. Reporting and cataloguing a number of ciliary mutant models, we discuss the importance of primary cilia for aRG function and cortical development.
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10
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Guo Y, Chomiak A, Hong Y, Lowe CC, Kopsidas CA, Chan WC, Andrade J, Pan H, Zhou X, Monuki ES, Feng Y. Histone H2A ubiquitination resulting from Brap loss of function connects multiple aging hallmarks and accelerates neurodegeneration. iScience 2022; 25:104519. [PMID: 35754718 PMCID: PMC9213774 DOI: 10.1016/j.isci.2022.104519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/06/2022] [Accepted: 05/29/2022] [Indexed: 01/10/2023] Open
Abstract
Aging is an intricate process characterized by multiple hallmarks including stem cell exhaustion, genome instability, epigenome alteration, impaired proteostasis, and cellular senescence. Whereas each of these traits is detrimental at the cellular level, it remains unclear how they are interconnected to cause systemic organ deterioration. Here we show that abrogating Brap, a BRCA1-associated protein essential for neurogenesis, results in persistent DNA double-strand breaks and elevation of histone H2A mono- and poly-ubiquitination (H2Aub). These defects extend to cellular senescence and proteasome-mediated histone H2A proteolysis with alterations in cells' proteomic and epigenetic states. Brap deletion in the mouse brain causes neuroinflammation, impaired proteostasis, accelerated neurodegeneration, and substantially shortened the lifespan. We further show the elevation of H2Aub also occurs in human brain tissues with Alzheimer's disease. These data together suggest that chromatin aberrations mediated by H2Aub may act as a nexus of multiple aging hallmarks and promote tissue-wide degeneration.
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Affiliation(s)
- Yan Guo
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Alison.A. Chomiak
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Ye Hong
- University of Turku, Turku 20500, Finland
| | - Clara C. Lowe
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Caroline A. Kopsidas
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Wen-Ching Chan
- Center for Research Informatics, University of Chicago, Chicago, IL 60637, USA
| | - Jorge Andrade
- Center for Research Informatics, University of Chicago, Chicago, IL 60637, USA
| | - Hongna Pan
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Xiaoming Zhou
- Department of Medicine, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Edwin S. Monuki
- Department of Pathology & Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Yuanyi Feng
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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11
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Novel DCX pathogenic variant in a girl with subcortical band heterotopia. REV ROMANA MED LAB 2022. [DOI: 10.2478/rrlm-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Subcortical band heterotopia (SBH), is a brain malformation defined by symmetrical and bilateral heterotopic gray matter bands localized deep within the white matter, between the cortex and lateral ventricles. SBH is the result of abnormal neuronal migration, with improper positioning of the cortical neurons. DCX gene (doublecortin), a microtubule-associated protein with essential roles in neuronal migration and differentiation during brain development, is one of the main contributors to the X-linked Lissencephaly spectrum pathogenesis (OMIM #300067). DCX variants are responsible for SBH in females and isolated lissencephaly in males. Herein, we present a 7-year-old girl with a de novo frameshift variant in DCX gene, unreported by date. The patient has focal complex seizures with onset at 23 months of age, fully controlled with medication, mild tremor and coordination impairment of fine movements and some learning difficulties, otherwise with normal development. The brain magnetic resonance imaging revealed the presence of thick SBH. Direct sequencing of DCX gene revealed a pathogenic heterozygous cytosine duplication in exon 3; this frameshift variant leads to a premature stop codon in position 164 (p.Gln160Profs*5). The variant type and its predicted consequence at protein level correlates with the severity of radiological findings. The clinical presentation of our patient is, however, milder than expected. Our research expands the mutational spectrum of DCX gene in SBH females and provides a detailed clinical and imagistic description of the patient. This paper highlights the utility of single gene sequencing as a first-tier diagnostic test of patients with gene-specific phenotypic features.
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12
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Nde1 is Required for Heterochromatin Compaction and Stability in Neocortical Neurons. iScience 2022; 25:104354. [PMID: 35601919 PMCID: PMC9121328 DOI: 10.1016/j.isci.2022.104354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
The NDE1 gene encodes a scaffold protein essential for brain development. Although biallelic NDE1 loss of function (LOF) causes microcephaly with profound mental retardation, NDE1 missense mutations and copy number variations are associated with multiple neuropsychiatric disorders. However, the etiology of the diverse phenotypes resulting from NDE1 aberrations remains elusive. Here we demonstrate Nde1 controls neurogenesis through facilitating H4K20 trimethylation-mediated heterochromatin compaction. This mechanism patterns diverse chromatin landscapes and stabilizes constitutive heterochromatin of neocortical neurons. We demonstrate that NDE1 can undergo dynamic liquid-liquid phase separation, partitioning to the nucleus and interacting with pericentromeric and centromeric satellite repeats. Nde1 LOF results in nuclear architecture aberrations and DNA double-strand breaks, as well as instability and derepression of pericentromeric satellite repeats in neocortical neurons. These findings uncover a pivotal role of NDE1/Nde1 in establishing and protecting neuronal heterochromatin. They suggest that heterochromatin instability predisposes a wide range of brain dysfunction. Cortical neurogenesis is coupled with heterochromatin compaction marked by H4K20me3 Nde1 undergoes liquid-liquid phase separation and interacts with heterochromatin Nde1 mutations impair H4K20me3 during neural progenitor differentiation Neurons lacking Nde1 derepress heterochromatin and lose nuclear and genomic integrity
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13
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Garrott SR, Gillies JP, DeSantis ME. Nde1 and Ndel1: Outstanding Mysteries in Dynein-Mediated Transport. Front Cell Dev Biol 2022; 10:871935. [PMID: 35493069 PMCID: PMC9041303 DOI: 10.3389/fcell.2022.871935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
Cytoplasmic dynein-1 (dynein) is the primary microtubule minus-end directed molecular motor in most eukaryotes. As such, dynein has a broad array of functions that range from driving retrograde-directed cargo trafficking to forming and focusing the mitotic spindle. Dynein does not function in isolation. Instead, a network of regulatory proteins mediate dynein’s interaction with cargo and modulate dynein’s ability to engage with and move on the microtubule track. A flurry of research over the past decade has revealed the function and mechanism of many of dynein’s regulators, including Lis1, dynactin, and a family of proteins called activating adaptors. However, the mechanistic details of two of dynein’s important binding partners, the paralogs Nde1 and Ndel1, have remained elusive. While genetic studies have firmly established Nde1/Ndel1 as players in the dynein transport pathway, the nature of how they regulate dynein activity is unknown. In this review, we will compare Ndel1 and Nde1 with a focus on discerning if the proteins are functionally redundant, outline the data that places Nde1/Ndel1 in the dynein transport pathway, and explore the literature supporting and opposing the predominant hypothesis about Nde1/Ndel1’s molecular effect on dynein activity.
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Affiliation(s)
- Sharon R. Garrott
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - John P. Gillies
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Morgan E. DeSantis
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Morgan E. DeSantis,
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14
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Deficiency of nde1 in zebrafish induces brain inflammatory responses and autism-like behavior. iScience 2022; 25:103876. [PMID: 35243238 PMCID: PMC8861649 DOI: 10.1016/j.isci.2022.103876] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/10/2022] [Accepted: 02/01/2022] [Indexed: 12/27/2022] Open
Abstract
The cytoskeletal protein NDE1 plays an important role in chromosome segregation, neural precursor differentiation, and neuronal migration. Clinical studies have shown that NDE1 deficiency is associated with several neuropsychiatric disorders including autism. Here, we generated nde1 homologous deficiency zebrafish (nde1−/−) to elucidate the cellular molecular mechanisms behind it. nde1−/− exhibit increased neurological apoptotic responses at early infancy, enlarged ventricles, and shrank valvula cerebelli in adult brain tissue. Behavioral analysis revealed that nde1−/− displayed autism-like behavior traits such as increased locomotor activity and repetitive stereotype behaviors and impaired social and kin recognition behaviors. Furthermore, nde1 mRNA injection rescued apoptosis in early development, and minocycline treatment rescued impaired social behavior and overactive motor activity by inhibiting inflammatory cytokines. In this study, we revealed that nde1 homozygous deletion leads to abnormal neurological development with autism-related behavioral phenotypes and that inflammatory responses in the brain are an important molecular basis behind it. nde1−/− zebrafish display autism-like behavior features nde1 deficiency results in immune responses in the brain Minocycline treatment inhibits immune responses in the adult nde1−/− brain Minocycline rescued the impaired social behavior and locomotor activity
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15
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Buttermore ED, Anderson NC, Chen PF, Makhortova NR, Kim KH, Wafa SMA, Dwyer S, Micozzi JM, Winden KD, Zhang B, Han MJ, Kleiman RJ, Brownstein CA, Sahin M, Gonzalez-Heydrich J. 16p13.11 deletion variants associated with neuropsychiatric disorders cause morphological and synaptic changes in induced pluripotent stem cell-derived neurons. Front Psychiatry 2022; 13:924956. [PMID: 36405918 PMCID: PMC9669751 DOI: 10.3389/fpsyt.2022.924956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
16p13.11 copy number variants (CNVs) have been associated with autism, schizophrenia, psychosis, intellectual disability, and epilepsy. The majority of 16p13.11 deletions or duplications occur within three well-defined intervals, and despite growing knowledge of the functions of individual genes within these intervals, the molecular mechanisms that underlie commonly observed clinical phenotypes remain largely unknown. Patient-derived, induced pluripotent stem cells (iPSCs) provide a platform for investigating the morphological, electrophysiological, and gene-expression changes that result from 16p13.11 CNVs in human-derived neurons. Patient derived iPSCs with varying sizes of 16p13.11 deletions and familial controls were differentiated into cortical neurons for phenotypic analysis. High-content imaging and morphological analysis of patient-derived neurons demonstrated an increase in neurite branching in patients compared with controls. Whole-transcriptome sequencing revealed expression level changes in neuron development and synaptic-related gene families, suggesting a defect in synapse formation. Subsequent quantification of synapse number demonstrated increased numbers of synapses on neurons derived from early-onset patients compared to controls. The identification of common phenotypes among neurons derived from patients with overlapping 16p13.11 deletions will further assist in ascertaining common pathways and targets that could be utilized for screening drug candidates. These studies can help to improve future treatment options and clinical outcomes for 16p13.11 deletion patients.
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Affiliation(s)
- Elizabeth D Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Nickesha C Anderson
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Pin-Fang Chen
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Nina R Makhortova
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Kristina H Kim
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Syed M A Wafa
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Sean Dwyer
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - John M Micozzi
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Kellen D Winden
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Min-Joon Han
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Robin J Kleiman
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Catherine A Brownstein
- The Manton Center of Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Mustafa Sahin
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Joseph Gonzalez-Heydrich
- Department of Psychiatry, Developmental Neuropsychiatry Research Program, Boston Children's Hospital, Boston, MA, United States
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16
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Bas H, Saylisoy S, Cilingir O, Gokalp EE, Kocagil S, Yarar C, Aras BD, Artan S. NDE1-related disorders: A recurrent NDE1 pathogenic variant causing Lissencephaly 4 can also be associated with microhydranencephaly. Am J Med Genet A 2021; 188:326-331. [PMID: 34562061 DOI: 10.1002/ajmg.a.62508] [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: 05/03/2021] [Revised: 08/06/2021] [Accepted: 09/04/2021] [Indexed: 11/08/2022]
Abstract
NudE Neurodevelopment Protein 1 (NDE1) gene encodes a protein required for microtubule organization, mitosis, and neuronal migration. Biallelic pathogenic variants of NDE1 gene are associated with structural central nervous system abnormalities, specifically microlissencephaly and microhydranencephaly. The root of these different phenotypes remains unclear. Here, we report a 20-year-old male patient referred to our clinics due to severe microcephaly, developmental delay, spastic quadriplegia, and dysmorphic features. The cranial computed tomography revealed abnormal brain structure and excess of cerebrospinal fluid, consistent with microhydranencephaly. A homozygous c.684_685del, p.(Pro229TrpfsTer85) change in NDE1 gene was found by clinical exome analysis. The variant has previously been reported in individuals with microlissencephaly, therefore we propose that the same variant within the gene may cause either microlissencephaly or microhydranencephaly phenotypes. There are only a few papers about NDE1-related disorders in the literature and the patient we described is important to clarify the phenotypic spectrum of the disease.
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Affiliation(s)
- Hasan Bas
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskişehir, Turkey
| | - Suzan Saylisoy
- Faculty of Medicine, Department of Radiology, Eskisehir Osmangazi University, Eskişehir, Turkey
| | - Oguz Cilingir
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskişehir, Turkey
| | - Ebru Erzurumluoglu Gokalp
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskişehir, Turkey
| | - Sinem Kocagil
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskişehir, Turkey
| | - Coskun Yarar
- Faculty of Medicine, Department of Pediatric Neurology, Eskisehir Osmangazi University, Eskişehir, Turkey
| | - Beyhan Durak Aras
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskişehir, Turkey
| | - Sevilhan Artan
- Faculty of Medicine, Department of Medical Genetics, Eskisehir Osmangazi University, Eskişehir, Turkey
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17
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Xu J, Deng X, Wu X, Zhu H, Zhu Y, Liu J, Chen Q, Yuan C, Liu G, Wang C. Primary cilia regulate gastric cancer-induced bone loss via cilia/Wnt/β-catenin signaling pathway. Aging (Albany NY) 2021; 13:8989-9010. [PMID: 33690174 PMCID: PMC8034975 DOI: 10.18632/aging.202734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022]
Abstract
Cancer-associated bone disease is a frequent occurrence in cancer patients and is associated with pain, bone fragility, loss, and fractures. However, whether primary or non-bone metastatic gastric cancer induces bone loss remains unclear. Here, we collected clinical evidence of bone loss by analyzing serum and X-rays of 25 non-bone metastatic gastric cancer patients. In addition, C57BL mice were injected with the human gastric cancer cell line HGC27 and its effect on bone mass was analyzed by Micro-CT, immunoblotting, and immunohistochemistry. Furthermore, the degree of the proliferation and osteogenic differentiation of mesenchymal stem cells (MSCs) co-cultured with HGC-27 or SGC-7901 cells was analyzed by colony-formation assay, alizarin red staining, immunofluorescence, qPCR, immunoblotting, and alkaline phosphatase activity assay. These indicated that gastric cancer could damage bone tissue before the occurrence of bone metastases. We also found that cilia formation of MSCs was increased in the presence of HGC27 cells, which was associated with abnormal activation of the Wnt/β-catenin pathway. Expression of DKK1 inhibited the Wnt/β-catenin signaling pathway and partially rescued osteogenic differentiation of MSCs. In summary, our results suggest that gastric cancer cells might cause bone damage prior to the occurrence of bone metastasis via cilia-dependent activation of the Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Jie Xu
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoyan Deng
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiangmei Wu
- Department of Physiology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Huifang Zhu
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yinghua Zhu
- Department of Pre-Hospital Emergency, Chongqing Emergency Medical Center, Central Hospital of Chongqing University, Chongqing 400014, China
| | - Jie Liu
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Qian Chen
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Chengfu Yuan
- College of Medical Science, China Three Gorges University, Yichang 443002, Hubei, China
| | - Geli Liu
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Changdong Wang
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
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18
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Gavrilovici C, Jiang Y, Kiroski I, Sterley TL, Vandal M, Bains J, Park SK, Rho JM, Teskey GC, Nguyen MD. Behavioral Deficits in Mice with Postnatal Disruption of Ndel1 in Forebrain Excitatory Neurons: Implications for Epilepsy and Neuropsychiatric Disorders. Cereb Cortex Commun 2021; 2:tgaa096. [PMID: 33615226 PMCID: PMC7876307 DOI: 10.1093/texcom/tgaa096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/11/2020] [Accepted: 12/28/2020] [Indexed: 12/30/2022] Open
Abstract
Dysfunction of nuclear distribution element-like 1 (Ndel1) is associated with schizophrenia, a neuropsychiatric disorder characterized by cognitive impairment and with seizures as comorbidity. The levels of Ndel1 are also altered in human and models with epilepsy, a chronic condition whose hallmark feature is the occurrence of spontaneous recurrent seizures and is typically associated with comorbid conditions including learning and memory deficits, anxiety, and depression. In this study, we analyzed the behaviors of mice postnatally deficient for Ndel1 in forebrain excitatory neurons (Ndel1 CKO) that exhibit spatial learning and memory deficits, seizures, and shortened lifespan. Ndel1 CKO mice underperformed in species-specific tasks, that is, the nest building, open field, Y maze, forced swim, and dry cylinder tasks. We surveyed the expression and/or activity of a dozen molecules related to Ndel1 functions and found changes that may contribute to the abnormal behaviors. Finally, we tested the impact of Reelin glycoprotein that shows protective effects in the hippocampus of Ndel1 CKO, on the performance of the mutant animals in the nest building task. Our study highlights the importance of Ndel1 in the manifestation of species-specific animal behaviors that may be relevant to our understanding of the clinical conditions shared between neuropsychiatric disorders and epilepsy.
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Affiliation(s)
- Cezar Gavrilovici
- Departments of Neurosciences & Pediatrics, University of California San Diego, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Yulan Jiang
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, and Biochemistry and Molecular Biology, Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
| | - Ivana Kiroski
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, and Biochemistry and Molecular Biology, Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
| | - Toni-Lee Sterley
- Departments of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Milene Vandal
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, and Biochemistry and Molecular Biology, Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
| | - Jaideep Bains
- Departments of Physiology and Pharmacology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jong M Rho
- Departments of Neurosciences & Pediatrics, University of California San Diego, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - G Campbell Teskey
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
| | - Minh Dang Nguyen
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, and Biochemistry and Molecular Biology, Hotchkiss Brain Institute, Calgary, AB T2N 4N1, Canada
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19
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Brock S, Cools F, Jansen AC. Neuropathology of genetically defined malformations of cortical development-A systematic literature review. Neuropathol Appl Neurobiol 2021; 47:585-602. [PMID: 33480109 PMCID: PMC8359484 DOI: 10.1111/nan.12696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/31/2020] [Accepted: 01/15/2021] [Indexed: 12/23/2022]
Abstract
AIMS Malformations of cortical development (MCD) include a heterogeneous spectrum of clinical, imaging, molecular and histopathological entities. While the understanding of genetic causes of MCD has improved with the availability of next-generation sequencing modalities, genotype-histopathological correlations remain limited. This is the first systematic review of molecular and neuropathological findings in patients with MCD to provide a comprehensive overview of the literature. METHODS A systematic review was performed between November 2019 and February 2020. A MEDLINE search was conducted for 132 genes previously linked to MCD in order to identify studies reporting macroscopic and/or microscopic findings in patients with a confirmed genetic cause. RESULTS Eighty-one studies were included in this review reporting neuropathological features associated with pathogenic variants in 46 genes (46/132 genes, 34.8%). Four groups emerged, consisting of (1) 13 genes with well-defined histological-genotype correlations, (2) 27 genes for which neuropathological reports were limited, (3) 5 genes with conflicting neuropathological features, and (4) 87 genes for which no histological data were available. Lissencephaly and polymicrogyria were reported most frequently. Associated brain malformations were variably present, with abnormalities of the corpus callosum as most common associated feature. CONCLUSIONS Neuropathological data in patients with MCD with a defined genetic cause are available only for a small number of genes. As each genetic cause might lead to unique histopathological features of MCD, standardised thorough neuropathological assessment and reporting should be encouraged. Histological features can help improve the understanding of the pathogenesis of MCD and generate hypotheses with impact on further research directions.
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Affiliation(s)
- Stefanie Brock
- Department of Pathology, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium.,Neurogenetics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Filip Cools
- Department of Neonatology, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Anna C Jansen
- Neurogenetics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Pediatric Neurology Unit, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
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20
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The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis. Nat Commun 2021; 12:821. [PMID: 33547282 PMCID: PMC7865055 DOI: 10.1038/s41467-021-21064-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Down syndrome is associated with genome-wide perturbation of gene expression, which may be mediated by epigenetic changes. We perform an epigenome-wide association study on neonatal bloodspots comparing 196 newborns with Down syndrome and 439 newborns without Down syndrome, adjusting for cell-type heterogeneity, which identifies 652 epigenome-wide significant CpGs (P < 7.67 × 10−8) and 1,052 differentially methylated regions. Differential methylation at promoter/enhancer regions correlates with gene expression changes in Down syndrome versus non-Down syndrome fetal liver hematopoietic stem/progenitor cells (P < 0.0001). The top two differentially methylated regions overlap RUNX1 and FLI1, both important regulators of megakaryopoiesis and hematopoietic development, with significant hypermethylation at promoter regions of these two genes. Excluding Down syndrome newborns harboring preleukemic GATA1 mutations (N = 30), identified by targeted sequencing, has minimal impact on the epigenome-wide association study results. Down syndrome has profound, genome-wide effects on DNA methylation in hematopoietic cells in early life, which may contribute to the high frequency of hematological problems, including leukemia, in children with Down syndrome. Down syndrome has a high co-morbidity with immune and hematopoietic disorders. Here, the authors perform an epigenome-wide association study in newborns with and without Down syndrome to find differential methylation across the genome, including in hematopoietic regulators RUNX1 and FLI1.
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21
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Soto-Perez J, Baumgartner M, Kanadia RN. Role of NDE1 in the Development and Evolution of the Gyrified Cortex. Front Neurosci 2020; 14:617513. [PMID: 33390896 PMCID: PMC7775536 DOI: 10.3389/fnins.2020.617513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/12/2020] [Indexed: 12/17/2022] Open
Abstract
An expanded cortex is a hallmark of human neurodevelopment and endows increased cognitive capabilities. Recent work has shown that the cell cycle-related gene NDE1 is essential for proper cortical development. Patients who have mutations in NDE1 exhibit congenital microcephaly as a primary phenotype. At the cellular level, NDE1 is essential for interkinetic nuclear migration and mitosis of radial glial cells, which translates to an indispensable role in neurodevelopment. The nuclear migration function of NDE1 is well conserved across Opisthokonta. In mammals, multiple isoforms containing alternate terminal exons, which influence the functionality of NDE1, have been reported. It has been noted that the pattern of terminal exon usage mirrors patterns of cortical complexity in mammals. To provide context to these findings, here, we provide a comprehensive review of the literature regarding NDE1, its molecular biology and physiological relevance at the cellular and organismal levels. In particular, we outline the potential roles of NDE1 in progenitor cell behavior and explore the spectrum of NDE1 pathogenic variants. Moreover, we assessed the evolutionary conservation of NDE1 and interrogated whether the usage of alternative terminal exons is characteristic of species with gyrencephalic cortices. We found that gyrencephalic species are more likely to express transcripts that use the human-associated terminal exon, whereas lissencephalic species tend to express transcripts that use the mouse-associated terminal exon. Among gyrencephalic species, the human-associated terminal exon was preferentially expressed by those with a high order of gyrification. These findings underscore phylogenetic relationships between the preferential usage of NDE1 terminal exon and high-order gyrification, which provide insight into cortical evolution underlying high-order brain functions.
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Affiliation(s)
- Jaseph Soto-Perez
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | | | - Rahul N. Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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22
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Aviel-Shekler K, Hamshawi Y, Sirhan W, Getselter D, Srikanth KD, Malka A, Piran R, Elliott E. Gestational diabetes induces behavioral and brain gene transcription dysregulation in adult offspring. Transl Psychiatry 2020; 10:412. [PMID: 33239620 PMCID: PMC7688640 DOI: 10.1038/s41398-020-01096-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/19/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023] Open
Abstract
The etiology of Autism Spectrum Disorders (ASD) includes a strong genetic component and a complicated environmental component. Recent evidence indicates that maternal diabetes, including gestational diabetes, is associated with an increased prevalence of ASD. While previous studies have looked into possible roles for maternal diabetes in neurodevelopment, there are few studies into how gestational diabetes, with no previous diabetic or metabolic phenotype, may affect neurodevelopment. In this study, we have specifically induced gestational diabetes in mice, followed by behavioral and molecular phenotyping of the mice offspring. Pregnant mice were injected with STZ a day after initiation of pregnancy. Glucose levels increased to diabetic levels between E7 and E14 in pregnancy in a subset of the pregnant animals. Male offspring of Gestational Diabetic mothers displayed increased repetitive behaviors with no dysregulation in the three-chambered social interaction test. RNA-seq analysis revealed a dysregulation in genes related to forebrain development in the frontal cortex and a dysregulation of a network of neurodevelopment and immune related genes in the striatum. Together, these results give evidence that gestational diabetes can induce changes in adulthood behavior and gene transcription in the brain.
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Affiliation(s)
- Keren Aviel-Shekler
- grid.22098.310000 0004 1937 0503Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Yara Hamshawi
- grid.22098.310000 0004 1937 0503Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Worood Sirhan
- grid.22098.310000 0004 1937 0503Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Dmitriy Getselter
- grid.22098.310000 0004 1937 0503Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Kolluru D. Srikanth
- grid.22098.310000 0004 1937 0503Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Assaf Malka
- grid.22098.310000 0004 1937 0503Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Ron Piran
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
| | - Evan Elliott
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
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23
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Omoto T, Takahashi T, Fujimori K, Kin S. Prenatal diagnosis of fetal microhydranencephaly: a case report and literature review. BMC Pregnancy Childbirth 2020; 20:688. [PMID: 33176733 PMCID: PMC7661269 DOI: 10.1186/s12884-020-03400-1] [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: 09/09/2020] [Accepted: 11/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The prenatal diagnosis of microhydranencephaly is important and needs to be distinguished from anencephaly, because unlike anencephaly, fetuses with microhydranencephaly can survive after birth. Herein, we report a case of microhydranencephaly that was diagnosed and distinguished from anencephaly prenatally. CASE PRESENTATION The patient was an 18-year-old woman, 2 gravida nullipara, who presented at 15 weeks of gestation. Ultrasonography showed a normal biparietal diameter (BPD) and no major anomalies. At 23 weeks of gestation, an ultrasound examination revealed a BPD of 40 mm (-5.3 standard deviation, SD). At 29 weeks, anencephaly was suspected despite difficulty in visually examining the fetal head above the orbit. At 34 weeks, insertion of a metreurynter made it possible to observe the skull. Three-dimensional computed tomography (CT) and magnetic resonance imaging (MRI) confirmed the presence of the fetal skull, a prominent occipital bone, sloping forehead, marked microcephaly, cerebral loss, and excess cerebrospinal fluid. This allowed differentiation between microhydranencephaly and anencephaly. She delivered vaginally at 37 weeks, and the child had a birth weight of 2342 g and a head circumference of 24 cm (-5.4 SD). The baby's head was flat above the forehead, with a suspected partial head defect. The baby received desmopressin acetate due to central diabetes insipidus 6 months after birth. CONCLUSIONS The use of multiple imaging modalities and physical manipulation of the fetal head are required to accurately differentiate between microhydranencephaly and anencephaly.
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Affiliation(s)
- Takahiro Omoto
- Department of Obstetrics and Gynecology, Takeda General Hospital, 965- 8585, Aidu Wakamatsu, Japan.,Department of Obstetrics and Gynecology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, 960-1295, Fukushima City, Japan
| | - Toshifumi Takahashi
- Fukushima Medical Center for Children and Women, Fukushima Medical University, 1 Hikarigaoka, 960-1295, Fukushima City, Japan.
| | - Keiya Fujimori
- Department of Obstetrics and Gynecology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, 960-1295, Fukushima City, Japan
| | - Shogo Kin
- Department of Obstetrics and Gynecology, Takeda General Hospital, 965- 8585, Aidu Wakamatsu, Japan
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24
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Surapaneni SK, Bhat ZR, Tikoo K. MicroRNA-941 regulates the proliferation of breast cancer cells by altering histone H3 Ser 10 phosphorylation. Sci Rep 2020; 10:17954. [PMID: 33087811 PMCID: PMC7578795 DOI: 10.1038/s41598-020-74847-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/25/2020] [Indexed: 12/25/2022] Open
Abstract
Breast cancer including triple negative breast cancer (TNBC) represents an important clinical challenge, as these tumours often develop resistance to conventional chemotherapeutics. MicroRNAs play a crucial role in cell-cycle regulation, differentiation, apoptosis, and migration. Herein, we performed Affymetrix Gene Chip miRNA 4.0 microarray and observed differential regulation of miRNAs (75 upregulated and 199 downregulated) in metastatic MDA-MB-231 cells as compared to immortalized human non-tumorigenic breast epithelial (MCF-10A) cells. MicroRNA-941 was significantly upregulated in MDA-MB-231 cells (almost nine-fold increase) in comparison to MCF-10A cells. Transfection of MiRNA-941 inhibitor significantly decreased the proliferation and migration of MDA-MB-231 cells by altering the expressions of p21, Cyclin D1, PP2B-B1, E-cadherin and MMP-13. Interestingly, we provide first evidence that inhibiting miR-941 prevents cell proliferation and phosphorylation of histone H3 at Ser10 residue. Xenograft model of breast cancer was developed by subcutaneous injection of MDA-MB-231 cells into the mammary fat pad of female athymic nude mice (Crl:NU-Foxn1nu). The tumours were allowed to grow to around 60 mm3, thereafter which we divided the animals into seven groups (n = 5). Notably, intratumoral injection of miR-941 inhibitor significantly abolished the tumour growth in MDA-MB-231 xenograft model. 5-Fluorouracil (10 mg/kg, i.p.) was used as positive control in our study. To the best of our knowledge, we report for the first time that targeting miR-941 improves the sensitivity of MDA-MB-231 cells to 5-fluorouracil. This can be of profound clinical significance, as it provides novel therapeutic approach for treating variety of cancers (overexpressing miRNA-941) in general and breast cancers in particular.
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Affiliation(s)
- Sunil Kumar Surapaneni
- Laboratory of Epigenetics and Diseases, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar, Sahibzada Ajit Singh Nagar, India
| | - Zahid Rafiq Bhat
- Laboratory of Epigenetics and Diseases, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar, Sahibzada Ajit Singh Nagar, India
| | - Kulbhushan Tikoo
- Laboratory of Epigenetics and Diseases, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar, Sahibzada Ajit Singh Nagar, India.
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25
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Cabet S, Guibaud L, Sanlaville D. [Microlissencephaly due to pathogenic variants of NDE1: from pathology to normal brain development]. Med Sci (Paris) 2020; 36:866-871. [PMID: 33026328 DOI: 10.1051/medsci/2020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pathogenic variants of the gene NDE1 (Nuclear Distribution Element 1) in humans lead to microlissencephaly which associates a reduced head circumference and a simplified gyration. Microlissencephaly is the most severe deficit of neurogenesis described to date but its precise physiopathological mechanism is not yet well known. The NDE1 gene encodes a phosphoprotein that is essential to neurogenesis and that is expressed in various cell compartments of neuroblasts. More than 60 interaction partners with NDE1 have been reported, notably various proteins involved in formation of the mitotic spindle, in ciliation, in genome protection of dividing neuroblasts or even in apoptosis (like LIS1, dynein or cohesin), which are all avenues that we explore in this review.
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Affiliation(s)
- Sara Cabet
- Service de génétique, Hospices Civils de Lyon, groupement hospitalier Est, France - Service de radiologie, Hospices Civils de Lyon, groupement hospitalier Est, 59 boulevard Pinel, 69677 Bron Cedex, France
| | - Laurent Guibaud
- Service de radiologie, Hospices Civils de Lyon, groupement hospitalier Est, 59 boulevard Pinel, 69677 Bron Cedex, France
| | - Damien Sanlaville
- Service de génétique, Hospices Civils de Lyon, groupement hospitalier Est, France - Inserm U1028, CNRS UMR5292, équipe GENDEV, Centre de recherche en neurosciences de Lyon, 69000 Lyon, France
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26
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Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell 2020; 182:685-712.e19. [PMID: 32645325 PMCID: PMC7321036 DOI: 10.1016/j.cell.2020.06.034] [Citation(s) in RCA: 677] [Impact Index Per Article: 169.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
Abstract
The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.
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Affiliation(s)
- Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Miguel Correa Marrero
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Svenja Ulferts
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erica Stevenson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ajda Rojc
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Alexandra Hardy
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Rémy Robinot
- Virus & Immunity Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France; Vaccine Research Institute, 94000 Creteil, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | | | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alistair Dunham
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sebastian Weigang
- Institute of Virology, Medical Center - University of Freiburg, Freiburg 79104, Germany
| | - Julian Knerr
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diego Quintero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Alberto Valdeolivas
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Trupti Patil
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gwendolyn Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sophia Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anna Gaulton
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emma J Manners
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eloy Félix
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Marisa Goff
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jean K Lim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | | | | | | | - Emmie De Wit
- NIH/NIAID/Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Andrew R Leach
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - R Dyche Mullins
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | | | - Georg Kochs
- Institute of Virology, Medical Center - University of Freiburg, Freiburg 79104, Germany; Faculty of Medicine, University of Freiburg, Freiburg 79008, Germany
| | - Robert Grosse
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany; Faculty of Medicine, University of Freiburg, Freiburg 79008, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg 79104, Germany.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France.
| | - Jeffery R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute.
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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27
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Powell SK, O'Shea CP, Shannon SR, Akbarian S, Brennand KJ. Investigation of Schizophrenia with Human Induced Pluripotent Stem Cells. ADVANCES IN NEUROBIOLOGY 2020; 25:155-206. [PMID: 32578147 DOI: 10.1007/978-3-030-45493-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Schizophrenia is a chronic and severe neuropsychiatric condition manifested by cognitive, emotional, affective, perceptual, and behavioral abnormalities. Despite decades of research, the biological substrates driving the signs and symptoms of the disorder remain elusive, thus hampering progress in the development of treatments aimed at disease etiologies. The recent emergence of human induced pluripotent stem cell (hiPSC)-based models has provided the field with a highly innovative approach to generate, study, and manipulate living neural tissue derived from patients, making possible the exploration of fundamental roles of genes and early-life stressors in disease-relevant cell types. Here, we begin with a brief overview of the clinical, epidemiological, and genetic aspects of the condition, with a focus on schizophrenia as a neurodevelopmental disorder. We then highlight relevant technical advancements in hiPSC models and assess novel findings attained using hiPSC-based approaches and their implications for disease biology and treatment innovation. We close with a critical appraisal of the developments necessary for both further expanding knowledge of schizophrenia and the translation of new insights into therapeutic innovations.
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Affiliation(s)
- Samuel K Powell
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Callan P O'Shea
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara Rose Shannon
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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28
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Chen TH, Boughal H. A penalized structural equation modeling method accounting for secondary phenotypes for variable selection on genetically regulated expression from PrediXcan for Alzheimer's disease. Biometrics 2020; 77:362-371. [PMID: 32339261 DOI: 10.1111/biom.13286] [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: 03/19/2019] [Revised: 03/13/2020] [Accepted: 04/13/2020] [Indexed: 12/01/2022]
Abstract
As the global burden of mental illness is estimated to become a severe issue in the near future, it demands the development of more effective treatments. Most psychiatric diseases are moderately to highly heritable and believed to involve many genes. Development of new treatment options demands more knowledge on the molecular basis of psychiatric diseases. Toward this end, we propose to develop new statistical methods with improved sensitivity and accuracy to identify disease-related genes specialized for psychiatric diseases. The qualitative psychiatric diagnoses such as case control often suffer from high rates of misdiagnosis and oversimplify the disease phenotypes. Our proposed method utilizes endophenotypes, the quantitative traits hypothesized to underlie disease syndromes, to better characterize the heterogeneous phenotypes of psychiatric diseases. We employ the structural equation modeling using the liability-index model to link multiple genetically regulated expressions from PrediXcan and the manifest variables including endophenotypes and case-control status. The proposed method can be considered as a general method for multivariate regression, which is particularly helpful for psychiatric diseases. We derive penalized retrospective likelihood estimators to deal with the typical small sample size issue. Simulation results demonstrate the advantages of the proposed method and the real data analysis of Alzheimer's disease illustrates the practical utility of the techniques. Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative database.
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Affiliation(s)
- Ting-Huei Chen
- Département de mathématiques et de statistique, Université Laval, Québec, Canada.,Cervo Brain Research Centre, Québec, Canada
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29
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Kodani A, Kenny C, Lai A, Gonzalez DM, Stronge E, Sejourne GM, Isacco L, Partlow JN, O'Donnell A, McWalter K, Byrne AB, Barkovich AJ, Yang E, Hill RS, Gawlinski P, Wiszniewski W, Cohen JS, Fatemi SA, Baranano KW, Sahin M, Vossler DG, Yuskaitis CJ, Walsh CA. Posterior Neocortex-Specific Regulation of Neuronal Migration by CEP85L Identifies Maternal Centriole-Dependent Activation of CDK5. Neuron 2020; 106:246-255.e6. [PMID: 32097629 PMCID: PMC7255387 DOI: 10.1016/j.neuron.2020.01.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/22/2019] [Accepted: 01/22/2020] [Indexed: 01/01/2023]
Abstract
Genes mutated in human neuronal migration disorders encode tubulin proteins and a variety of tubulin-binding and -regulating proteins, but it is very poorly understood how these proteins function together to coordinate migration. Additionally, the way in which regional differences in neocortical migration are controlled is completely unknown. Here we describe a new syndrome with remarkably region-specific effects on neuronal migration in the posterior cortex, reflecting de novo variants in CEP85L. We show that CEP85L is required cell autonomously in vivo and in vitro for migration, that it localizes to the maternal centriole, and that it forms a complex with many other proteins required for migration, including CDK5, LIS1, NDE1, KIF2A, and DYNC1H1. Loss of CEP85L disrupts CDK5 localization and activation, leading to centrosome disorganization and disrupted microtubule cytoskeleton organization. Together, our findings suggest that CEP85L highlights a complex that controls CDK5 activity to promote neuronal migration.
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Affiliation(s)
- Andrew Kodani
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
| | - Connor Kenny
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Abbe Lai
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Edward Stronge
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Gabrielle M Sejourne
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Laura Isacco
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Anne O'Donnell
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Alicia B Byrne
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia; School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - A James Barkovich
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - R Sean Hill
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Pawel Gawlinski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Wojciech Wiszniewski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Julie S Cohen
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Ali Fatemi
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristin W Baranano
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - David G Vossler
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Christopher J Yuskaitis
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
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30
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Barone R, Gulisano M, Amore R, Domini C, Milana MC, Giglio S, Madia F, Mattina T, Casabona A, Fichera M, Rizzo R. Clinical correlates in children with autism spectrum disorder and CNVs: Systematic investigation in a clinical setting. Int J Dev Neurosci 2020; 80:276-286. [PMID: 32159884 DOI: 10.1002/jdn.10024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 01/09/2023] Open
Abstract
Autism spectrum disorder (ASD) is associated with various molecular mechanisms including copy number variants (CNVs). We investigated possible associations between CNVs and ASD clinical correlates. We evaluated pertinent physical characteristics and phenotypic measures such as cognitive level, severity of ASD symptoms and comorbid conditions in ASD patients consecutively recruited over the study period. Children with causative (C-CNVs), non-causative (NC-CNVs) and without CNVs (W-CNVs) were compared. Out of 109 patients, 31 imbalances (16 duplications and 15 deletions) were detected in 25 subjects. Seven (6.4%) had C-CNVs and 18 (16.5%) had NC-CNVs. Paired post hoc comparisons with Bonferroni adjustment showed that dysmorphisms and microcephaly were significantly more frequent in the C-CNVs group. Patients with C-CNVs had more severe autistic core symptoms, while comorbid internalizing behavioral symptoms were more represented among participants with NC-CNVs. No significant differences were observed for distribution of macrocephaly, intellectual disability, epilepsy, isolated electroencephalogram abnormalities and studied neuroimaging characteristics among groups. Recurrent and rare C-CNVs highlighting genes relevant to neurodevelopment had a statistically higher occurrence in children with more severe ASD symptoms and further developmental abnormalities. This study documents the importance of measuring the physical and neurobehavioural correlates of ASD phenotypes to unravel the underlying molecular mechanisms in patient subgroups.
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Affiliation(s)
- Rita Barone
- Child Neuropsychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- CNR-Institute for Polymers, Composites and Biomaterials IPCB, Catania, Italy
| | - Mariangela Gulisano
- Child Neuropsychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Renata Amore
- Child Neuropsychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Carla Domini
- Child Neuropsychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Maria Chiara Milana
- Child Neuropsychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Meyer Children's Hospital, University of Florence, Firenze, Italy
| | - Francesca Madia
- Laboratory of Neurogenetics and Neuroscience, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Teresa Mattina
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | - Antonino Casabona
- Department of Biomedical and Biotechnological Sciences, Section of Physiology, University of Catania, Catania, Italy
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
- Oasi Research Institute-IRCCS, Troina, Italy
| | - Renata Rizzo
- Child Neuropsychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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31
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Mechanistic insights into the interactions of dynein regulator Ndel1 with neuronal ankyrins and implications in polarity maintenance. Proc Natl Acad Sci U S A 2019; 117:1207-1215. [PMID: 31889000 DOI: 10.1073/pnas.1916987117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ankyrin-G (AnkG), a highly enriched scaffold protein in the axon initial segment (AIS) of neurons, functions to maintain axonal polarity and the integrity of the AIS. At the AIS, AnkG regulates selective intracellular cargo trafficking between soma and axons via interaction with the dynein regulator protein Ndel1, but the molecular mechanism underlying this binding remains elusive. Here we report that Ndel1's C-terminal coiled-coil region (CT-CC) binds to giant neuron-specific insertion regions present in both AnkG and AnkB with 2:1 stoichiometry. The high-resolution crystal structure of AnkB in complex with Ndel1 CT-CC revealed the detailed molecular basis governing the AnkB/Ndel1 complex formation. Mechanistically, AnkB binds with Ndel1 by forming a stable 5-helix bundle dominated by hydrophobic interactions spread across 6 distinct interaction layers. Moreover, we found that AnkG is essential for Ndel1 accumulation at the AIS. Finally, we found that cargo sorting at the AIS can be disrupted by blocking the AnkG/Ndel1 complex formation using a peptide designed based on our structural data. Collectively, the atomic structure of the AnkB/Ndel1 complex together with studies of cargo sorting through the AIS establish the mechanistic basis for AnkG/Ndel1 complex formation and for the maintenance of axonal polarity. Our study will also be valuable for future studies of the interaction between AnkB and Ndel1 perhaps at distal axonal cargo transport.
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32
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Pruski M, Hu L, Yang C, Wang Y, Zhang JB, Zhang L, Huang Y, Rajnicek AM, St Clair D, McCaig CD, Lang B, Ding YQ. Roles for IFT172 and Primary Cilia in Cell Migration, Cell Division, and Neocortex Development. Front Cell Dev Biol 2019; 7:287. [PMID: 31850339 PMCID: PMC6890611 DOI: 10.3389/fcell.2019.00287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/04/2019] [Indexed: 12/25/2022] Open
Abstract
The cilium of a cell translates varied extracellular cues into intracellular signals that control embryonic development and organ function. The dynamic maintenance of ciliary structure and function requires balanced bidirectional cargo transport involving intraflagellar transport (IFT) complexes. IFT172 is a member of the IFT complex B, and IFT172 mutation is associated with pathologies including short rib thoracic dysplasia, retinitis pigmentosa and Bardet-Biedl syndrome, but how it underpins these conditions is not clear. We used the WIM cell line, derived from embryonic fibroblasts of Wimple mice (carrying homozygous Leu1564Pro mutation in Ift172), to probe roles of Ift172 and primary cilia in cell behavior. WIM cells had ablated cilia and deficiencies in directed migration (electrotaxis), cell proliferation and intracellular signaling. Additionally, WIM cells displayed altered cell cycle progression, with increased numbers of chromatids, highlighting dysfunctional centrosome status. Exposure to a physiological electric field promoted a higher percentage of primary cilia in wild-type cells. Interestingly, in situ hybridization revealed an extensive and dynamic expression profile of Ift172 in both developing and adult mouse cortex. In vivo manipulation of Ift172 expression in germinal regions of embryonic mouse brains perturbed neural progenitor proliferation and radial migration of post-mitotic neurons, revealing a regulatory role of Ift172 in cerebral morphogenesis. Our data suggest that Ift172 regulates a range of fundamental biological processes, highlighting the pivotal roles of the primary cilium in cell physiology and brain development.
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Affiliation(s)
- Michal Pruski
- Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Mental Disorders, Changsha, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.,Key Laboratory of Arrhythmias, Ministry of Education, East Hospital, Department of Anatomy and Neurobiology, Collaborative Innovation Centre for Brain Science, Tongji University School of Medicine, Shanghai, China.,School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ling Hu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.,School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Cuiping Yang
- Key Laboratory of Arrhythmias, Ministry of Education, East Hospital, Department of Anatomy and Neurobiology, Collaborative Innovation Centre for Brain Science, Tongji University School of Medicine, Shanghai, China
| | - Yubing Wang
- Key Laboratory of Arrhythmias, Ministry of Education, East Hospital, Department of Anatomy and Neurobiology, Collaborative Innovation Centre for Brain Science, Tongji University School of Medicine, Shanghai, China
| | - Jin-Bao Zhang
- Department of Histology and Embryology, Institute of Neuroscience, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Arrhythmias, Ministry of Education, East Hospital, Department of Anatomy and Neurobiology, Collaborative Innovation Centre for Brain Science, Tongji University School of Medicine, Shanghai, China.,School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ying Huang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.,Key Laboratory of Arrhythmias, Ministry of Education, East Hospital, Department of Anatomy and Neurobiology, Collaborative Innovation Centre for Brain Science, Tongji University School of Medicine, Shanghai, China.,School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ann M Rajnicek
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - David St Clair
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Colin D McCaig
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Bing Lang
- Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Mental Disorders, Changsha, China.,School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Yu-Qiang Ding
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.,Key Laboratory of Arrhythmias, Ministry of Education, East Hospital, Department of Anatomy and Neurobiology, Collaborative Innovation Centre for Brain Science, Tongji University School of Medicine, Shanghai, China
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33
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López-Escardó D, Grau-Bové X, Guillaumet-Adkins A, Gut M, Sieracki ME, Ruiz-Trillo I. Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190088. [PMID: 31587642 PMCID: PMC6792448 DOI: 10.1098/rstb.2019.0088] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2019] [Indexed: 12/25/2022] Open
Abstract
Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need the broadest taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand our understanding of the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangement processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal protein domains that are essential to the maintenance of animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- David López-Escardó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Amy Guillaumet-Adkins
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | | | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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34
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Submicroscopic aberrations of chromosome 16 in prenatal diagnosis. Mol Cytogenet 2019; 12:36. [PMID: 31391865 PMCID: PMC6681493 DOI: 10.1186/s13039-019-0448-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/10/2019] [Indexed: 12/27/2022] Open
Abstract
Background Nearly 9.89% of chromosome 16 consists of segmental duplications, which makes it prone to non-homologous recombination. The present study aimed to investigate the incidence and perinatal characteristics of submicroscopic chromosome 16 aberrations in prenatal diagnosis. Results A total of 2,414 consecutive fetuses that underwent prenatal chromosomal microarray analysis (CMA) between January 2016 and December 2018 were reviewed. Submicroscopic anomalies of chromosome 16 accounted for 11.1% (15/134) of all submicroscopic anomalies detected in fetuses with normal karyotype, which was larger than the percentage of anomalies in any other chromosome. The 15 submicroscopic anomalies of chromosome 16 were identified in 14 cases; 12 of them had ultrasound abnormalities. They were classified as pathogenic (N = 7), and variants of uncertain significance (N = 8). Seven fetuses with variants of uncertain significance were ended in live-born, and the remaining were end in pregnancy termination. Conclusion Submicroscopic aberrations of chromosome 16 are frequent findings in prenatal diagnosis, which emphasize the challenge of genetic counseling and the value of CMA. Prenatal diagnosis should lead to long-term monitoring of children with such chromosomal abnormalities for better understanding of the phenotype of chromosome 16 microdeletion and microduplication syndromes.
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Thomas S, Boutaud L, Reilly ML, Benmerah A. Cilia in hereditary cerebral anomalies. Biol Cell 2019; 111:217-231. [DOI: 10.1111/boc.201900012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Thomas
- Laboratory of Embryology and Genetics of Human MalformationINSERM UMR 1163Paris Descartes UniversityImagine Institute 75015 Paris France
| | - Lucile Boutaud
- Laboratory of Embryology and Genetics of Human MalformationINSERM UMR 1163Paris Descartes UniversityImagine Institute 75015 Paris France
| | - Madeline Louise Reilly
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163Paris Descartes UniversityImagine Institute 75015 Paris France
- Paris Diderot University 75013 Paris France
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, INSERM UMR 1163Paris Descartes UniversityImagine Institute 75015 Paris France
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Pruski M, Lang B. Primary Cilia-An Underexplored Topic in Major Mental Illness. Front Psychiatry 2019; 10:104. [PMID: 30886591 PMCID: PMC6409319 DOI: 10.3389/fpsyt.2019.00104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/12/2019] [Indexed: 12/20/2022] Open
Abstract
Though much progress has been made in recent years towards understanding the function and physiology of primary cilia, they remain a somewhat elusive organelle. Some studies have explored the role of primary cilia in the developing nervous system, and their dysfunction has been linked with several neurosensory deficits. Yet, very little has been written on their potential role in psychiatric disorders. This article provides an overview of some of the functions of primary cilia in signalling pathways, and demonstrates that they are a worthy candidate in psychiatric research. The links between primary cilia and major mental illness have been demonstrated to exist at several levels, spanning genetics, signalling pathways, and pharmacology as well as cell division and migration. The primary focus of this review is on the sensory role of the primary cilium and the neurodevelopmental hypothesis of psychiatric disease. As such, the primary cilium is demonstrated to be a key link between the cellular environment and cell behaviour, and hence of key importance in the considerations of the nature and nurture debate in psychiatric research.
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Affiliation(s)
- Michal Pruski
- Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
- Critical Care Laboratory, Critical Care Directorate, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- School of Healthcare Science, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
| | - Bing Lang
- Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, China
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Xiang Y, Ye Y, Lou Y, Yang Y, Cai C, Zhang Z, Mills T, Chen NY, Kim Y, Muge Ozguc F, Diao L, Karmouty-Quintana H, Xia Y, Kellems RE, Chen Z, Blackburn MR, Yoo SH, Shyu AB, Mills GB, Han L. Comprehensive Characterization of Alternative Polyadenylation in Human Cancer. J Natl Cancer Inst 2019; 110:379-389. [PMID: 29106591 DOI: 10.1093/jnci/djx223] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 09/20/2017] [Indexed: 12/16/2022] Open
Abstract
Background Alternative polyadenylation (APA) is emerging as a major post-transcriptional mechanism for gene regulation, and dysregulation of APA contributes to several human diseases. However, the functional consequences of APA in human cancer are not fully understood. Particularly, there is no large-scale analysis in cancer cell lines. Methods We characterized the global APA profiles of 6398 patient samples across 17 cancer types from The Cancer Genome Atlas and 739 cancer cell lines from the Cancer Cell Line Encyclopedia. We built a linear regression model to explore the correlation between APA factors and APA events across different cancer types. We used Spearman correlation to assess the effects of APA events on drug sensitivity and the Wilcoxon rank-sum test or Cox proportional hazards model to identify clinically relevant APA events. Results We revealed a striking global 3'UTR shortening in cancer cell lines compared with tumor samples. Our analysis further suggested PABPN1 as the master regulator in regulating APA profile across different cancer types. Furthermore, we showed that APA events could affect drug sensitivity, especially of drugs targeting chromatin modifiers. Finally, we identified 1971 clinically relevant APA events, as well as alterations of APA in clinically actionable genes, suggesting that analysis of the complexity of APA profiles could have clinical utility. Conclusions Our study highlights important roles for APA in human cancer, including reshaping cellular pathways and regulating specific gene expression, exemplifying the complex interplay between APA and other biological processes and yielding new insights into the action mechanism of cancer drugs.
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Affiliation(s)
- Yu Xiang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yanyan Lou
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL
| | - Yang Yang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chunyan Cai
- Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Tingting Mills
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Ning-Yuan Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yoonjin Kim
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Fatma Muge Ozguc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Rodney E Kellems
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Michael R Blackburn
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX
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38
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Johnstone M, Vasistha NA, Barbu MC, Dando O, Burr K, Christopher E, Glen S, Robert C, Fetit R, Macleod KG, Livesey MR, Clair DS, Blackwood DHR, Millar K, Carragher NO, Hardingham GE, Wyllie DJA, Johnstone EC, Whalley HC, McIntosh AM, Lawrie SM, Chandran S. Reversal of proliferation deficits caused by chromosome 16p13.11 microduplication through targeting NFκB signaling: an integrated study of patient-derived neuronal precursor cells, cerebral organoids and in vivo brain imaging. Mol Psychiatry 2019; 24:294-311. [PMID: 30401811 PMCID: PMC6344377 DOI: 10.1038/s41380-018-0292-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 09/13/2018] [Accepted: 10/08/2018] [Indexed: 01/22/2023]
Abstract
The molecular basis of how chromosome 16p13.11 microduplication leads to major psychiatric disorders is unknown. Here we have undertaken brain imaging of patients carrying microduplications in chromosome 16p13.11 and unaffected family controls, in parallel with iPS cell-derived cerebral organoid studies of the same patients. Patient MRI revealed reduced cortical volume, and corresponding iPSC studies showed neural precursor cell (NPC) proliferation abnormalities and reduced organoid size, with the NPCs therein displaying altered planes of cell division. Transcriptomic analyses of NPCs uncovered a deficit in the NFκB p65 pathway, confirmed by proteomics. Moreover, both pharmacological and genetic correction of this deficit rescued the proliferation abnormality. Thus, chromosome 16p13.11 microduplication disturbs the normal programme of NPC proliferation to reduce cortical thickness due to a correctable deficit in the NFκB signalling pathway. This is the first study demonstrating a biologically relevant, potentially ameliorable, signalling pathway underlying chromosome 16p13.11 microduplication syndrome in patient-derived neuronal precursor cells.
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Affiliation(s)
- Mandy Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK.
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
| | - Navneet A Vasistha
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Miruna C Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Owen Dando
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, UK
| | - Karen Burr
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
| | - Edward Christopher
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sophie Glen
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Christelle Robert
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rana Fetit
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kenneth G Macleod
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Matthew R Livesey
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Douglas H R Blackwood
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Kirsty Millar
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Giles E Hardingham
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, UK
| | - David J A Wyllie
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, UK
| | - Eve C Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Heather C Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Stephen M Lawrie
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK.
- Centre for Brain Development and Repair, Bangalore, India.
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Karzbrun E, Reiner O. Brain Organoids-A Bottom-Up Approach for Studying Human Neurodevelopment. Bioengineering (Basel) 2019; 6:E9. [PMID: 30669275 PMCID: PMC6466401 DOI: 10.3390/bioengineering6010009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/08/2019] [Accepted: 01/11/2019] [Indexed: 12/25/2022] Open
Abstract
Brain organoids have recently emerged as a three-dimensional tissue culture platform to study the principles of neurodevelopment and morphogenesis. Importantly, brain organoids can be derived from human stem cells, and thus offer a model system for early human brain development and human specific disorders. However, there are still major differences between the in vitro systems and in vivo development. This is in part due to the challenge of engineering a suitable culture platform that will support proper development. In this review, we discuss the similarities and differences of human brain organoid systems in comparison to embryonic development. We then describe how organoids are used to model neurodevelopmental diseases. Finally, we describe challenges in organoid systems and how to approach these challenges using complementary bioengineering techniques.
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Affiliation(s)
- Eyal Karzbrun
- Kavli Institute for Theoretical Physics and Department of Physics, University of California, Santa Barbara, CA 93106, USA.
| | - Orly Reiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel.
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40
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Abdel-Hamid MS, El-Dessouky SH, Ateya MI, Gaafar HM, Abdel-Salam GMH. Phenotypic spectrum of NDE1-related disorders: from microlissencephaly to microhydranencephaly. Am J Med Genet A 2019; 179:494-497. [PMID: 30637988 DOI: 10.1002/ajmg.a.61035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/11/2018] [Accepted: 12/11/2018] [Indexed: 01/17/2023]
Abstract
Biallelic variants in the NDE1 gene have been shown to occur in extreme microcephaly. Most of the patients displayed microlissencephaly but one with microhydranencephaly. We report on three sibs in which the brain MRI and CT scans demonstrated variable degree of reduced volume of cerebral hemispheres and ventriculomegaly. Further, they had agenesis of corpus callosum, cerebellar, and brainstem hypoplasia. Fetal ultrasound at 32 weeks' gestation of the third sib revealed severe micrencephaly with extensive hydranencephaly and an anomaly consistent with non cleaved (fused) thalami. Because of the fused thalami, the STIL gene was targeted initially but showed negative results. His postnatal MRI showed that the cerebral hemispheres are markedly reduced in size (with no definite frontal, parietal, or occipital lobes) and replaced by a large sac filled with CSF. An intact falx cerebri was identified. This extensive hydarencephaly led us to consider the NDE1 and to identify a novel homozygous nonsense variant (c.54G>A, p.W18*). The variability of the degree of brain malformations and the apparent fusion of the thalami were illusive and delayed the recognition of the genetic etiology. Our results provide the first antenatal description of this rare syndrome. Further, we expand the genetic architecture and the neuroradiologic phenotype of NDE1-related disorders.
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Affiliation(s)
- Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Sara H El-Dessouky
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | | | | | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
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41
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St Clair D, Johnstone M. Using mouse transgenic and human stem cell technologies to model genetic mutations associated with schizophrenia and autism. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0037. [PMID: 29352035 PMCID: PMC5790834 DOI: 10.1098/rstb.2017.0037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2017] [Indexed: 12/22/2022] Open
Abstract
Solid progress has occurred over the last decade in our understanding of the molecular genetic basis of neurodevelopmental disorders, and of schizophrenia and autism in particular. Although the genetic architecture of both disorders is far more complex than previously imagined, many key loci have at last been identified. This has allowed in vivo and in vitro technologies to be refined to model specific high-penetrant genetic loci involved in both disorders. Using the DISC1/NDE1 and CYFIP1/EIF4E loci as exemplars, we explore the opportunities and challenges of using animal models and human-induced pluripotent stem cell technologies to further understand/treat and potentially reverse the worst consequences of these debilitating disorders. This article is part of a discussion meeting issue ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists’.
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Affiliation(s)
- David St Clair
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Mandy Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK.,Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
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42
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Vezain M, Lecuyer M, Rubio M, Dupé V, Ratié L, David V, Pasquier L, Odent S, Coutant S, Tournier I, Trestard L, Adle-Biassette H, Vivien D, Frébourg T, Gonzalez BJ, Laquerrière A, Saugier-Veber P. A de novo variant in ADGRL2 suggests a novel mechanism underlying the previously undescribed association of extreme microcephaly with severely reduced sulcation and rhombencephalosynapsis. Acta Neuropathol Commun 2018; 6:109. [PMID: 30340542 PMCID: PMC6195752 DOI: 10.1186/s40478-018-0610-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/29/2018] [Indexed: 12/13/2022] Open
Abstract
Extreme microcephaly and rhombencephalosynapsis represent unusual pathological conditions, each of which occurs in isolation or in association with various other cerebral and or extracerebral anomalies. Unlike microcephaly for which several disease-causing genes have been identified with different modes of inheritance, the molecular bases of rhombencephalosynapsis remain unknown and rhombencephalosynapsis presents mainly as a sporadic condition consistent with de novo dominant variations. We report for the first time the association of extreme microcephaly with almost no sulcation and rhombencephalosynapsis in a fœtus for which comparative patient-parent exome sequencing strategy revealed a heterozygous de novo missense variant in the ADGRL2 gene. ADGRL2 encodes latrophilin 2, an adhesion G-protein-coupled receptor whose exogenous ligand is α-latrotoxin. Adgrl2 immunohistochemistry and in situ hybridization revealed expression in the telencephalon, mesencephalon and rhombencephalon of mouse and chicken embryos. In human brain embryos and fœtuses, Adgrl2 immunoreactivity was observed in the hemispheric and cerebellar germinal zones, the cortical plate, basal ganglia, pons and cerebellar cortex. Microfluorimetry experiments evaluating intracellular calcium release in response to α-latrotoxin binding showed significantly reduced cytosolic calcium release in the fœtus amniocytes vs amniocytes from age-matched control fœtuses and in HeLa cells transfected with mutant ADGRL2 cDNA vs wild-type construct. Embryonic lethality was also observed in constitutive Adgrl2−/− mice. In Adgrl2+/− mice, MRI studies revealed microcephaly and vermis hypoplasia. Cell adhesion and wound healing assays demonstrated that the variation increased cell adhesion properties and reduced cell motility. Furthermore, HeLa cells overexpressing mutant ADGRL2 displayed a highly developed cytoplasmic F-actin network related to cytoskeletal dynamic modulation. ADGRL2 is the first gene identified as being responsible for extreme microcephaly with rhombencephalosynapsis. Increased cell adhesion, reduced cell motility and cytoskeletal dynamic alterations induced by the variant therefore represent a new mechanism responsible for microcephaly.
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43
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Calhoun JD, Carvill GL. Unravelling the genetic architecture of autosomal recessive epilepsy in the genomic era. J Neurogenet 2018; 32:295-312. [PMID: 30247086 DOI: 10.1080/01677063.2018.1513509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The technological advancement of next-generation sequencing has greatly accelerated the pace of variant discovery in epilepsy. Despite an initial focus on autosomal dominant epilepsy due to the tractable nature of variant discovery with trios under a de novo model, more and more variants are being reported in families with epilepsies consistent with autosomal recessive (AR) inheritance. In this review, we touch on the classical AR epilepsy variants such as the inborn errors of metabolism and malformations of cortical development. However, we also highlight recently reported genes that are being identified by next-generation sequencing approaches and online 'matchmaking' platforms. Syndromes mainly characterized by seizures and complex neurodevelopmental disorders comorbid with epilepsy are discussed as an example of the wide phenotypic spectrum associated with the AR epilepsies. We conclude with a foray into the future, from the application of whole-genome sequencing to identify elusive epilepsy variants, to the promise of precision medicine initiatives to provide novel targeted therapeutics specific to the individual based on their clinical genetic testing.
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Affiliation(s)
- Jeffrey D Calhoun
- a Department of Neurology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Gemma L Carvill
- a Department of Neurology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
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44
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Tan AP, Chong WK, Mankad K. Comprehensive genotype-phenotype correlation in lissencephaly. Quant Imaging Med Surg 2018; 8:673-693. [PMID: 30211035 DOI: 10.21037/qims.2018.08.08] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Malformations of cortical development (MCD) are a heterogenous group of disorders with diverse genotypic and phenotypic variations. Lissencephaly is a subtype of MCD caused by defect in neuronal migration, which occurs between 12 and 24 weeks of gestation. The continuous advancement in the field of molecular genetics in the last decade has led to identification of at least 19 lissencephaly-related genes, most of which are related to microtubule structural proteins (tubulin) or microtubule-associated proteins (MAPs). The aim of this review article is to bring together current knowledge of gene mutations associated with lissencephaly and to provide a comprehensive genotype-phenotype correlation. Illustrative cases will be presented to facilitate the understanding of the described genotype-phenotype correlation.
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Affiliation(s)
- Ai Peng Tan
- Department of Diagnostic Imaging, National University Health System, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore
| | - Wui Khean Chong
- Department of Neuroradiology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
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45
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Monda JK, Cheeseman IM. Nde1 promotes diverse dynein functions through differential interactions and exhibits an isoform-specific proteasome association. Mol Biol Cell 2018; 29:2336-2345. [PMID: 30024347 PMCID: PMC6249811 DOI: 10.1091/mbc.e18-07-0418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Nde1 is a key regulator of cytoplasmic dynein, binding directly to both dynein itself and the dynein adaptor, Lis1. Nde1 and Lis1 are thought to function together to promote dynein function, yet mutations in each result in distinct neurodevelopment phenotypes. To reconcile these phenotypic differences, we sought to dissect the contribution of Nde1 to dynein regulation and explore the cellular functions of Nde1. Here we show that an Nde1–Lis1 interaction is required for spindle pole focusing and Golgi organization but is largely dispensable for centrosome placement, despite Lis1 itself being required. Thus, diverse functions of dynein rely on distinct Nde1- and Lis1-mediated regulatory mechanisms. Additionally, we discovered a robust, isoform-specific interaction between human Nde1 and the 26S proteasome and identify precise mutations in Nde1 that disrupt the proteasome interaction. Together, our work suggests that Nde1 makes unique contributions to human neurodevelopment through its regulation of both dynein and proteasome function.
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Affiliation(s)
- Julie K Monda
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
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46
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Bradshaw NJ, Ukkola-Vuoti L, Pankakoski M, Zheutlin AB, Ortega-Alonso A, Torniainen-Holm M, Sinha V, Therman S, Paunio T, Suvisaari J, Lönnqvist J, Cannon TD, Haukka J, Hennah W. The NDE1 genomic locus can affect treatment of psychiatric illness through gene expression changes related to microRNA-484. Open Biol 2018; 7:rsob.170153. [PMID: 29142105 PMCID: PMC5717342 DOI: 10.1098/rsob.170153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/09/2017] [Indexed: 01/16/2023] Open
Abstract
Genetic studies of familial schizophrenia in Finland have observed significant associations with a group of biologically related genes, DISC1, NDE1, NDEL1, PDE4B and PDE4D, the ‘DISC1 network’. Here, we use gene expression and psychoactive medication use data to study their biological consequences and potential treatment implications. Gene expression levels were determined in 64 individuals from 18 families, while prescription medication information has been collected over a 10-year period for 931 affected individuals. We demonstrate that the NDE1 SNP rs2242549 associates with significant changes in gene expression for 2908 probes (2542 genes), of which 794 probes (719 genes) were replicable. A significant number of the genes altered were predicted targets of microRNA-484 (p = 3.0 × 10−8), located on a non-coding exon of NDE1. Variants within the NDE1 locus also displayed significant genotype by gender interaction to early cessation of psychoactive medications metabolized by CYP2C19. Furthermore, we demonstrate that miR-484 can affect the expression of CYP2C19 in a cell culture system. Thus, variation at the NDE1 locus may alter risk of mental illness, in part through modification of miR-484, and such modification alters treatment response to specific psychoactive medications, leading to the potential for use of this locus in targeting treatment.
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Affiliation(s)
- Nicholas J Bradshaw
- Department of Neuropathology, Heinrich Heine University, 40225 Düsseldorf, Germany.,Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Liisa Ukkola-Vuoti
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, Finland.,Medicum, Clinicum, University of Helsinki, 00014 Helsinki, Finland
| | - Maiju Pankakoski
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland
| | | | - Alfredo Ortega-Alonso
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, Finland
| | - Minna Torniainen-Holm
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, Finland
| | - Vishal Sinha
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, Finland.,Medicum, Clinicum, University of Helsinki, 00014 Helsinki, Finland
| | - Sebastian Therman
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Tiina Paunio
- Genomics and Biomarkers Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland.,Department of Psychiatry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - Jaana Suvisaari
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Jouko Lönnqvist
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland.,Department of Psychiatry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - Tyrone D Cannon
- Department of Psychology, Yale University, New Haven, CT 06520, USA
| | - Jari Haukka
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland.,Department of Public Health, Clinicum, University of Helsinki, 00014 Helsinki, Finland
| | - William Hennah
- Mental Health Unit, Department of Health, National Institute for Health and Welfare, 00271 Helsinki, Finland .,Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00014 Helsinki, Finland.,Medicum, Clinicum, University of Helsinki, 00014 Helsinki, Finland
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47
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Abstract
Primary microcephaly (MCPH, for "microcephaly primary hereditary") is a disorder of brain development that results in a head circumference more than 3 standard deviations below the mean for age and gender. It has a wide variety of causes, including toxic exposures, in utero infections, and metabolic conditions. While the genetic microcephaly syndromes are relatively rare, studying these syndromes can reveal molecular mechanisms that are critical in the regulation of neural progenitor cells, brain size, and human brain evolution. Many of the causative genes for MCPH encode centrosomal proteins involved in centriole biogenesis. However, other MCPH genes fall under different mechanistic categories, notably DNA replication and repair. Recent gene discoveries and functional studies have implicated novel cellular processes, such as cytokinesis, centromere and kinetochore function, transmembrane or intracellular transport, Wnt signaling, and autophagy, as well as the apical polarity complex. Thus, MCPH genes implicate a wide variety of molecular and cellular mechanisms in the regulation of cerebral cortical size during development.
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Affiliation(s)
- Divya Jayaraman
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, Massachusetts 02115, USA.,Current affiliation: Boston Combined Residency Program (Child Neurology), Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| | - Byoung-Il Bae
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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48
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Dubourg C, Kim A, Watrin E, de Tayrac M, Odent S, David V, Dupé V. Recent advances in understanding inheritance of holoprosencephaly. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2018; 178:258-269. [PMID: 29785796 DOI: 10.1002/ajmg.c.31619] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022]
Abstract
Holoprosencephaly (HPE) is a complex genetic disorder of the developing forebrain characterized by high phenotypic and genetic heterogeneity. HPE was initially defined as an autosomal dominant disease, but recent research has shown that its mode of transmission is more complex. The past decade has witnessed rapid development of novel genetic technologies and significant progresses in clinical studies of HPE. In this review, we recapitulate genetic epidemiological studies of the largest European HPE cohort and summarize the novel genetic discoveries of HPE based on recently developed diagnostic methods. Our main purpose is to present different inheritance patterns that exist for HPE with a particular emphasis on oligogenic inheritance and its implications in genetic counseling.
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Affiliation(s)
- Christèle Dubourg
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Artem Kim
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France
| | - Erwan Watrin
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France
| | - Marie de Tayrac
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Sylvie Odent
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Clinique, CHU, Rennes, France
| | - Véronique David
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Valérie Dupé
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France
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49
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Genetics and mechanisms leading to human cortical malformations. Semin Cell Dev Biol 2018; 76:33-75. [DOI: 10.1016/j.semcdb.2017.09.031] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
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50
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A genome-scale RNAi screen for genetic interactors of the dynein co-factor nud-2 in Caenorhabditis elegans. Sci Data 2018; 5:180047. [PMID: 29557975 PMCID: PMC5859877 DOI: 10.1038/sdata.2018.47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/01/2018] [Indexed: 12/22/2022] Open
Abstract
Cytoplasmic dynein 1 (dynein) is the predominant microtubule minus end-directed motor in animals and participates in a wide range of cellular processes, including membrane trafficking, nuclear migration, and cell division. Dynein's functional diversity depends on co-factors that regulate its subcellular localization, interaction with cargo, and motor activity. The ubiquitous co-factor nuclear distribution gene E (NudE) is implicated in many of dynein's functions, and mutations in NudE cause the brain developmental disease microcephaly. To identify genetic interactors of the Caenorhabditis elegans NudE homolog nud-2, we performed a genome-wide RNAi screen with the null allele nud-2(ok949), which compromises dynein function but leaves animals viable and fertile. Using bacterial feeding to deliver dsRNAs in a 96-well liquid format and a semi-automated fluorescence microscopy approach for counting parents and progeny, we screened 19762 bacterial clones and identified 38 genes whose inhibition caused enhanced lethality in nud-2(ok949) relative to the nud-2(+) control. Further study of these genes, many of which participate in cell division, promises to provide insight into the function and regulation of dynein.
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