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Pedicone C, Weitzman SA, Renton AE, Goate AM. Unraveling the complex role of MAPT-containing H1 and H2 haplotypes in neurodegenerative diseases. Mol Neurodegener 2024; 19:43. [PMID: 38812061 PMCID: PMC11138017 DOI: 10.1186/s13024-024-00731-x] [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: 09/30/2023] [Accepted: 05/11/2024] [Indexed: 05/31/2024] Open
Abstract
A ~ 1 Mb inversion polymorphism exists within the 17q21.31 locus of the human genome as direct (H1) and inverted (H2) haplotype clades. This inversion region demonstrates high linkage disequilibrium, but the frequency of each haplotype differs across ancestries. While the H1 haplotype exists in all populations and shows a normal pattern of genetic variability and recombination, the H2 haplotype is enriched in European ancestry populations, is less frequent in African ancestry populations, and nearly absent in East Asian ancestry populations. H1 is a known risk factor for several neurodegenerative diseases, and has been associated with many other traits, suggesting its importance in cellular phenotypes of the brain and entire body. Conversely, H2 is protective for these diseases, but is associated with predisposition to recurrent microdeletion syndromes and neurodevelopmental disorders such as autism. Many single nucleotide variants and copy number variants define H1/H2 haplotypes and sub-haplotypes, but identifying the causal variant(s) for specific diseases and phenotypes is complex due to the extended linkage equilibrium. In this review, we assess the current knowledge of this inversion region regarding genomic structure, gene expression, cellular phenotypes, and disease association. We discuss recent discoveries and challenges, evaluate gaps in knowledge, and highlight the importance of understanding the effect of the 17q21.31 haplotypes to promote advances in precision medicine and drug discovery for several diseases.
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Affiliation(s)
- Chiara Pedicone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah A Weitzman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan E Renton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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2
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Alomairah H, Ali A, Altemaimi R, Alabduljalil T. Uncommon fundus presentation of Koolen-De Vries Syndrome in a young boy. Ophthalmic Genet 2024; 45:164-166. [PMID: 37528764 DOI: 10.1080/13816810.2023.2237573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
INTRODUCTION Koleen-De Vries syndrome (KDVS) is a rare genetic condition characterized by typical facial features, intellectual disability, cardiac and renal diseases, and ophthalmic manifestations. The syndrome is known to be caused by a microdeletion in the 17q21.31 region, involving multiple genes, including the KANSL1 gene. CASE PRESENTATION We present the case of a 9-year-old boy with no family history of ophthalmic syndromes. The patient exhibited bilateral hypopigmented iris and unilateral choroidal and retinal pigment epithelium (RPE) hypopigmentation. DISCUSSION The presence of ophthalmic manifestations, such as bilateral hypopigmented iris and unilateral choroidal and RPE hypopigmentation, in a patient with KDVS adds to the clinical spectrum of this syndrome. Although the exact mechanism underlying these ocular findings is not yet fully understood, the microdeletion in the 17q21.31 region, which includes the KANSL1 gene, is likely to play a role. CONCLUSION This case highlights the importance of considering ophthalmic manifestations in individuals diagnosed with Koleen-De Vries syndrome. Further research is needed to better understand the pathogenesis and clinical implications of these ocular findings.
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Affiliation(s)
| | | | - Rabeah Altemaimi
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Kuwait University, Kuwait
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3
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Awamleh Z, Choufani S, Wu W, Rots D, Dingemans AJM, Nadif Kasri N, Boronat S, Ibañez-Mico S, Cuesta Herraiz L, Ferrer I, Martínez Carrascal A, Pérez-Jurado LA, Aznar Lain G, Ortigoza-Escobar JD, de Vries BBA, Koolen DA, Weksberg R. A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells. Eur J Hum Genet 2024; 32:324-332. [PMID: 38282074 PMCID: PMC10923882 DOI: 10.1038/s41431-024-01538-6] [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: 09/22/2023] [Revised: 12/27/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
Pathogenic variants in KANSL1 and 17q21.31 microdeletions are causative of Koolen-de Vries syndrome (KdVS), a neurodevelopmental syndrome with characteristic facial dysmorphia. Our previous work has shown that syndromic conditions caused by pathogenic variants in epigenetic regulatory genes have identifiable patterns of DNA methylation (DNAm) change: DNAm signatures or episignatures. Given the role of KANSL1 in histone acetylation, we tested whether variants underlying KdVS are associated with a DNAm signature. We profiled whole-blood DNAm for 13 individuals with KANSL1 variants, four individuals with 17q21.31 microdeletions, and 21 typically developing individuals, using Illumina's Infinium EPIC array. In this study, we identified a robust DNAm signature of 456 significant CpG sites in 8 individuals with KdVS, a pattern independently validated in an additional 7 individuals with KdVS. We also demonstrate the diagnostic utility of the signature and classify two KANSL1 VUS as well as four variants in individuals with atypical clinical presentation. Lastly, we investigated tissue-specific DNAm changes in fibroblast cells from individuals with KdVS. Collectively, our findings contribute to the understanding of the epigenetic landscape related to KdVS and aid in the diagnosis and classification of variants in this structurally complex genomic region.
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Affiliation(s)
- Zain Awamleh
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Wendy Wu
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Dmitrijs Rots
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Susana Boronat
- Department of Pediatrics, Hospital del Santa Creu y Sant Pau, Barcelona, Spain
| | - Salvador Ibañez-Mico
- Department of Pediatric Neurology, Hospital Virgen de la Arrixaca, Murcia, Madrid, Spain
| | | | - Irene Ferrer
- Department of Genetics, Consorcio Hospital General de Valencia, Valencia, Spain
| | | | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and CIBERER, Barcelona, Spain
| | - Gemma Aznar Lain
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and CIBERER, Barcelona, Spain
| | - Juan Dario Ortigoza-Escobar
- Movement Disorders Unit, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Bert B A de Vries
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands.
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada.
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, the Hospital for Sick Children, University of Toronto, Toronto, ON, M5G 1×8, Canada.
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4
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Geller E, Noble MA, Morales M, Gockley J, Emera D, Uebbing S, Cotney JL, Noonan JP. Massively parallel disruption of enhancers active in human neural stem cells. Cell Rep 2024; 43:113693. [PMID: 38271204 PMCID: PMC11078116 DOI: 10.1016/j.celrep.2024.113693] [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: 02/03/2023] [Revised: 11/02/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Changes in gene regulation have been linked to the expansion of the human cerebral cortex and to neurodevelopmental disorders, potentially by altering neural progenitor proliferation. However, the effects of genetic variation within regulatory elements on neural progenitors remain obscure. We use sgRNA-Cas9 screens in human neural stem cells (hNSCs) to disrupt 10,674 genes and 26,385 conserved regions in 2,227 enhancers active in the developing human cortex and determine effects on proliferation. Genes with proliferation phenotypes are associated with neurodevelopmental disorders and show biased expression in specific fetal human brain neural progenitor populations. Although enhancer disruptions overall have weaker effects than gene disruptions, we identify enhancer disruptions that severely alter hNSC self-renewal. Disruptions in human accelerated regions, implicated in human brain evolution, also alter proliferation. Integrating proliferation phenotypes with chromatin interactions reveals regulatory relationships between enhancers and their target genes contributing to neurogenesis and potentially to human cortical evolution.
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Affiliation(s)
- Evan Geller
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mark A Noble
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Matheo Morales
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jake Gockley
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Justin L Cotney
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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5
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Lewerissa EI, Nadif Kasri N, Linda K. Epigenetic regulation of autophagy-related genes: Implications for neurodevelopmental disorders. Autophagy 2024; 20:15-28. [PMID: 37674294 PMCID: PMC10761153 DOI: 10.1080/15548627.2023.2250217] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionarily highly conserved catabolic process that is important for the clearance of cytosolic contents to maintain cellular homeostasis and survival. Recent findings point toward a critical role for autophagy in brain function, not only by preserving neuronal health, but especially by controlling different aspects of neuronal development and functioning. In line with this, mutations in autophagy-related genes are linked to various key characteristics and symptoms of neurodevelopmental disorders (NDDs), including autism, micro-/macrocephaly, and epilepsy. However, the group of NDDs caused by mutations in autophagy-related genes is relatively small. A significant proportion of NDDs are associated with mutations in genes encoding epigenetic regulatory proteins that modulate gene expression, so-called chromatinopathies. Intriguingly, several of the NDD-linked chromatinopathy genes have been shown to regulate autophagy-related genes, albeit in non-neuronal contexts. From these studies it becomes evident that tight transcriptional regulation of autophagy-related genes is crucial to control autophagic activity. This opens the exciting possibility that aberrant autophagic regulation might underly nervous system impairments in NDDs with disturbed epigenetic regulation. We here summarize NDD-related chromatinopathy genes that are known to regulate transcriptional regulation of autophagy-related genes. Thereby, we want to highlight autophagy as a candidate key hub mechanism in NDD-related chromatinopathies.Abbreviations: ADNP: activity dependent neuroprotector homeobox; ASD: autism spectrum disorder; ATG: AutTophaGy related; CpG: cytosine-guanine dinucleotide; DNMT: DNA methyltransferase; EHMT: euchromatic histone lysine methyltransferase; EP300: E1A binding protein p300; EZH2: enhancer of zeste 2 polycomb repressive complex 2 subunit; H3K4me3: histone 3 lysine 4 trimethylation; H3K9me1/2/3: histone 3 lysine 9 mono-, di-, or trimethylation; H3K27me2/3: histone 3 lysine 27 di-, or trimethylation; hiPSCs: human induced pluripotent stem cells; HSP: hereditary spastic paraplegia; ID: intellectual disability; KANSL1: KAT8 regulatory NSL complex subunit 1; KAT8: lysine acetyltransferase 8; KDM1A/LSD1: lysine demethylase 1A; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin complex 1; NDD: neurodevelopmental disorder; PHF8: PHD finger protein 8; PHF8-XLID: PHF8-X linked intellectual disability syndrome; PTM: post-translational modification; SESN2: sestrin 2; YY1: YY1 transcription factor; YY1AP1: YY1 associated protein 1.
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Affiliation(s)
- Elly I. Lewerissa
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, Nijmegen, Gelderland, The Netherlands
| | - Katrin Linda
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Gelderland, The Netherlands
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Flemish Brabant, Belgium
- Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Flemish Brabant, Belgium
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6
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Guhathakurta S, Erdogdu NU, Hoffmann JJ, Grzadzielewska I, Schendzielorz A, Seyfferth J, Mårtensson CU, Corrado M, Karoutas A, Warscheid B, Pfanner N, Becker T, Akhtar A. COX17 acetylation via MOF-KANSL complex promotes mitochondrial integrity and function. Nat Metab 2023; 5:1931-1952. [PMID: 37813994 PMCID: PMC10663164 DOI: 10.1038/s42255-023-00904-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/06/2023] [Indexed: 10/11/2023]
Abstract
Reversible acetylation of mitochondrial proteins is a regulatory mechanism central to adaptive metabolic responses. Yet, how such functionally relevant protein acetylation is achieved remains unexplored. Here we reveal an unprecedented role of the MYST family lysine acetyltransferase MOF in energy metabolism via mitochondrial protein acetylation. Loss of MOF-KANSL complex members leads to mitochondrial defects including fragmentation, reduced cristae density and impaired mitochondrial electron transport chain complex IV integrity in primary mouse embryonic fibroblasts. We demonstrate COX17, a complex IV assembly factor, as a bona fide acetylation target of MOF. Loss of COX17 or expression of its non-acetylatable mutant phenocopies the mitochondrial defects observed upon MOF depletion. The acetylation-mimetic COX17 rescues these defects and maintains complex IV activity even in the absence of MOF, suggesting an activatory role of mitochondrial electron transport chain protein acetylation. Fibroblasts from patients with MOF syndrome who have intellectual disability also revealed respiratory defects that could be restored by alternative oxidase, acetylation-mimetic COX17 or mitochondrially targeted MOF. Overall, our findings highlight the critical role of MOF-KANSL complex in mitochondrial physiology and provide new insights into MOF syndrome.
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Affiliation(s)
- Sukanya Guhathakurta
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Juliane J Hoffmann
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Iga Grzadzielewska
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Christoph U Mårtensson
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mauro Corrado
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Adam Karoutas
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bettina Warscheid
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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7
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Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serrano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. Nat Commun 2023; 14:5327. [PMID: 37723137 PMCID: PMC10507039 DOI: 10.1038/s41467-023-40348-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/20/2023] [Indexed: 09/20/2023] Open
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identify over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1526 and 3308 circRNAs are custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 29% of Parkinson's and 12% of Alzheimer's disease-associated genes produced validated circRNAs. circDNAJC6, which is transcribed from a juvenile-onset Parkinson's gene, is already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produce circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA-regulated synaptic specialization in neuropsychiatric diseases.
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Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- State Key Lab of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B Feany
- Departement of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA.
- Precision Neurology Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
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8
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Bouman A, Bouwmeester RN, van Vlimmeren LA, Burger P, Mandel JL, de Vries BBA, de Kleuver M, Klein WM, Geelen JM, Koolen DA. Clinical and radiological assessment of scoliosis in Koolen-de Vries syndrome. Am J Med Genet A 2023; 191:2346-2355. [PMID: 37350176 DOI: 10.1002/ajmg.a.63334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/23/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
Abstract
The Koolen-de Vries syndrome (KdVS) is a multisystem disorder characterized by developmental delay, intellectual disability, characteristic facial features, epilepsy, cardiovascular and urogenital malformations, and various musculoskeletal disorders. Scoliosis is a common feature. The aim of this study is to fill the gap in the current knowledge about scoliosis in individuals with KdVS and to provide recommendations for management and follow-up. In total, 54 individuals with KdVS were included in the study, with a mean age of 13.6 years (range 1.9-38.8 years). Spine radiographs, MR scans, and corresponding radiology reports were analyzed retrospectively for scoliosis and additional anomalies. The presence of scoliosis-related clinical conditions was assessed in participants' medical records and by use of a parent survey. Scoliosis was present in 56% of the participants (30/54) with a mean age of onset of 10.6 years and curve progression during the growth spurt. Prevalence at age 6, 10, and 18 years was, respectively, 9%, 41%, and 65%. Most participants were diagnosed with a single curve (13/24, 54%), of which five participants had a long C-curve type scoliosis. No significant risk factors for development of scoliosis could be identified. Severity was mostly classified as mild, although 29% (7/24) of the curves were larger than 30° at last follow-up. Bracing therapy was received in 13% (7/54), and surgical spinal fusion was warranted in 6% (3/54). Remarkably, participants with scoliosis received less often physical therapy compared to participants without scoliosis (P = 0.002). Scoliosis in individuals with KdVS should be closely monitored and radiologic screening for scoliosis and vertebrae abnormalities is recommended at diagnosis of KdVS, and the age of 10 and 18 years.
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Affiliation(s)
- Arianne Bouman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Romy N Bouwmeester
- Department of Pediatric Nephrology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Leo A van Vlimmeren
- Department of Rehabilitation and Pediatric Physical Therapy, Radboud University Medical Center, Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Pauline Burger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Neurogenetics and Translational Medicine, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg, Illkirch, France
| | - Jean-Louis Mandel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Neurogenetics and Translational Medicine, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg, Illkirch, France
- University of Strasbourg, Institute for Advanced Studies (USIAS), Strasbourg, France
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marinus de Kleuver
- Department of Orthopedic Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willemijn M Klein
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joyce M Geelen
- Developmental and Genetic Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
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9
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Iyer SS, Sun Y, Seyfferth J, Manjunath V, Samata M, Alexiadis A, Kulkarni T, Gutierrez N, Georgiev P, Shvedunova M, Akhtar A. The NSL complex is required for piRNA production from telomeric clusters. Life Sci Alliance 2023; 6:e202302194. [PMID: 37399316 PMCID: PMC10313855 DOI: 10.26508/lsa.202302194] [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: 05/31/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023] Open
Abstract
The NSL complex is a transcriptional activator. Germline-specific knockdown of NSL complex subunits NSL1, NSL2, and NSL3 results in reduced piRNA production from a subset of bidirectional piRNA clusters, accompanied by widespread transposon derepression. The piRNAs most transcriptionally affected by NSL2 and NSL1 RNAi map to telomeric piRNA clusters. At the chromatin level, these piRNA clusters also show decreased levels of H3K9me3, HP1a, and Rhino after NSL2 depletion. Using NSL2 ChIP-seq in ovaries, we found that this protein specifically binds promoters of telomeric transposons HeT-A, TAHRE, and TART Germline-specific depletion of NSL2 also led to a reduction in nuclear Piwi in nurse cells. Our findings thereby support a role for the NSL complex in promoting the transcription of piRNA precursors from telomeric piRNA clusters and in regulating Piwi levels in the Drosophila female germline.
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Affiliation(s)
- Shantanu S Iyer
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg im Breisgau, Germany
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Vinitha Manjunath
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Maria Samata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Anastasios Alexiadis
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Tanvi Kulkarni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Noel Gutierrez
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
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10
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Dingemans AJM, Hinne M, Truijen KMG, Goltstein L, van Reeuwijk J, de Leeuw N, Schuurs-Hoeijmakers J, Pfundt R, Diets IJ, den Hoed J, de Boer E, Coenen-van der Spek J, Jansen S, van Bon BW, Jonis N, Ockeloen CW, Vulto-van Silfhout AT, Kleefstra T, Koolen DA, Campeau PM, Palmer EE, Van Esch H, Lyon GJ, Alkuraya FS, Rauch A, Marom R, Baralle D, van der Sluijs PJ, Santen GWE, Kooy RF, van Gerven MAJ, Vissers LELM, de Vries BBA. PhenoScore quantifies phenotypic variation for rare genetic diseases by combining facial analysis with other clinical features using a machine-learning framework. Nat Genet 2023; 55:1598-1607. [PMID: 37550531 DOI: 10.1038/s41588-023-01469-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 07/05/2023] [Indexed: 08/09/2023]
Abstract
Several molecular and phenotypic algorithms exist that establish genotype-phenotype correlations, including facial recognition tools. However, no unified framework that investigates both facial data and other phenotypic data directly from individuals exists. We developed PhenoScore: an open-source, artificial intelligence-based phenomics framework, combining facial recognition technology with Human Phenotype Ontology data analysis to quantify phenotypic similarity. Here we show PhenoScore's ability to recognize distinct phenotypic entities by establishing recognizable phenotypes for 37 of 40 investigated syndromes against clinical features observed in individuals with other neurodevelopmental disorders and show it is an improvement on existing approaches. PhenoScore provides predictions for individuals with variants of unknown significance and enables sophisticated genotype-phenotype studies by testing hypotheses on possible phenotypic (sub)groups. PhenoScore confirmed previously known phenotypic subgroups caused by variants in the same gene for SATB1, SETBP1 and DEAF1 and provides objective clinical evidence for two distinct ADNP-related phenotypes, already established functionally.
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Affiliation(s)
- Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Artificial Intelligence, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Max Hinne
- Department of Artificial Intelligence, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Kim M G Truijen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lia Goltstein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Janneke Schuurs-Hoeijmakers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Illja J Diets
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joery den Hoed
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Elke de Boer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jet Coenen-van der Spek
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Noraly Jonis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Elizabeth E Palmer
- Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Gholson J Lyon
- Department of Human Genetics and George A. Jervis Clinic, Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
- Biology PhD Program, The Graduate Center, The City University of New York, New York City, NY, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anita Rauch
- Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Diana Baralle
- Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Marcel A J van Gerven
- Department of Artificial Intelligence, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
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11
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Lu Y, Zhou Y, Guo J, Qi M, Lin Y, Zhang X, Xiang Y, Fu Q, Wang B. Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies. Commun Biol 2023; 6:735. [PMID: 37460814 DOI: 10.1038/s42003-023-05101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are disorders resulting from defects in the development of the kidneys and their outflow tract. Copy number variations (CNVs) have been identified as important genetic variations leading to CAKUT, whereas most CAKUT-associated CNVs cannot be attributed to a specific pathogenic gene. Here we construct coexpression networks involving long noncoding RNAs (lncRNAs) within these CNVs (CNV-lncRNAs) using human kidney developmental transcriptomic data. The results show that CNV-lncRNAs encompassed in recurrent CAKUT associated CNVs have highly correlated expression with CAKUT genes in the developing kidneys. The regulatory effects of two hub CNV-lncRNAs (HSALNG0134318 in 22q11.2 and HSALNG0115943 in 17q12) in the module most significantly enriched in known CAKUT genes (CAKUT_sig1, P = 1.150 × 10-6) are validated experimentally. Our results indicate that the reduction of CNV-lncRNAs can downregulate CAKUT genes as predicted by our computational analyses. Furthermore, knockdown of HSALNG0134318 would downregulate HSALNG0115943 and affect kidney development related pathways. The results also indicate that the CAKUT_sig1 module has function significance involving multi-organ development. Overall, our findings suggest that CNV-lncRNAs play roles in regulating CAKUT genes, and the etiologies of CAKUT-associated CNVs should take account of effects on the noncoding genome.
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Affiliation(s)
- Yibo Lu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yiyang Zhou
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jing Guo
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ming Qi
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuwan Lin
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xingyu Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
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12
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Chen Z, Wu B, Li G, Zhou L, Zhang L, Liu J. MAPT rs17649553 T allele is associated with better verbal memory and higher small-world properties in Parkinson's disease. Neurobiol Aging 2023; 129:219-231. [PMID: 37413784 DOI: 10.1016/j.neurobiolaging.2023.06.006] [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: 03/08/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Currently, over 90 genetic loci have been found to be associated with Parkinson's disease (PD) in genome-wide association studies, nevertheless, the effects of these genetic variants on the clinical features and brain structure of PD patients are largely unknown. This study investigated the effects of microtubule-associated protein tau (MAPT) rs17649553 (C>T), a genetic variant associated with reduced PD risk, on the clinical manifestations and brain networks of PD patients. We found MAPT rs17649553 T allele was associated with better verbal memory in PD patients. In addition, MAPT rs17649553 significantly shaped the topology of gray matter covariance network and white matter network. Both the network metrics in gray matter covariance network and white matter network were correlated with verbal memory, however, the mediation analysis showed that it was the small-world properties in white matter network that mediated the effects of MAPT rs17649553 on verbal memory. These results suggest that MAPT rs17649553 T allele is associated with higher small-world properties in structural network and better verbal memory in PD.
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Affiliation(s)
- Zhichun Chen
- Department of Neurology and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Bin Wu
- Department of Neurology, Xuchang Central Hospital Affiliated with Henan University of Science and Technology, Henan, China
| | - Guanglu Li
- Department of Neurology and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Liche Zhou
- Department of Neurology and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lina Zhang
- Department of Biostatistics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Liu
- Department of Neurology and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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13
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St John M, van Reyk O, Koolen DA, de Vries BBA, Amor DJ, Morgan AT. Expanding the speech and language phenotype in Koolen-de Vries syndrome: late onset and periodic stuttering a novel feature. Eur J Hum Genet 2023; 31:531-540. [PMID: 36529818 PMCID: PMC10172335 DOI: 10.1038/s41431-022-01230-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Speech and language impairment is core in Koolen-de Vries syndrome (KdVS), yet only one study has examined this empirically. Here we define speech, language, and functional/adaptive behaviour in KdVS; while deeply characterising the medical/neurodevelopmental phenotype in the largest cohort to date. Speech, language, literacy, and social skills were assessed using standardised measures, alongside an in-depth health and medical questionnaire. 81 individuals with KdVS were recruited (35 female, mean age 9y 10mo), 56 of whom harboured the typical 500-650 kb 17q21.31 deletion. The core medical phenotype was intellectual disability (largely moderate), eye anomalies/vision disturbances, structural brain anomalies, dental problems, sleep disturbance, musculoskeletal abnormalities, and cardiac defects. Most were verbal (62/81, 76.5%), while minimally-verbal communicators used alternative and augmentative communication (AAC) successfully in spite of speech production delays. Speech was characterised by apraxia (39/61, 63.9%) and dysarthria (28/61, 45.9%) in verbal participants. Stuttering was described in 36/47 (76.6%) verbal participants and followed a unique trajectory of late onset and fluctuating presence. Receptive and expressive language abilities were commensurate with one another, but literacy skills remained a relative weakness. Social competence, successful behavioural/emotional control, and coping skills were areas of relative strength, while communication difficulties impacted daily living skills as an area of comparative difficulty. Notably, KdVS individuals make communication gains beyond childhood and should continue to access targeted therapies throughout development, including early AAC implementation, motor speech therapy, language/literacy intervention, as well as strategies implemented to successfully navigate activities of daily living that rely on effective communication.
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Affiliation(s)
- Miya St John
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Audiology and Speech Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Olivia van Reyk
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - David A Koolen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Angela T Morgan
- Murdoch Children's Research Institute, Parkville, VIC, Australia.
- Department of Audiology and Speech Pathology, University of Melbourne, Melbourne, VIC, Australia.
- Speech Pathology Department, Royal Children's Hospital, Melbourne, VIC, Australia.
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14
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Karamik G, Tuysuz B, Isik E, Yilmaz A, Alanay Y, Sunamak EC, Durmusalioglu EA, Ozkinay F, Cetin GO, Ozturk N, Mihci E, Nur B. The clinical phenotype of Koolen-de Vries syndrome in Turkish patients and literature review. Am J Med Genet A 2023. [PMID: 37053206 DOI: 10.1002/ajmg.a.63207] [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: 06/21/2022] [Revised: 12/28/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023]
Abstract
Koolen-de Vries syndrome (KdVS) is a rare multisystemic disorder caused by a microdeletion on chromosome 17q21.31 including KANSL1 gene or intragenic pathogenic variants in KANSL1 gene. Here, we describe the clinical and genetic spectrum of eight Turkish children with KdVS due to a de novo 17q21.31 deletion, and report on several rare/new conditions. Eight patients from unrelated families aged between 17 months and 19 years enrolled in this study. All patients evaluated by a clinical geneticist, and the clinical diagnosis were confirmed by molecular karyotyping. KdVS patients had some common distinctive facial features. All patients had neuromotor retardation, and speech and language delay. Epilepsy, structural brain anomalies, ocular, ectodermal, and musculoskeletal findings, and friendly personality were remarkable in more than half of the patients. Hypertension, hypothyroidism, celiac disease, and postaxial polydactyly were among the rare/new conditions. Our study contributes to the clinical spectrum of patients with KdVS, while also provide a review by comparing them with previous cohort studies.
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Affiliation(s)
- Gokcen Karamik
- Department of Pediatrics, Division of Pediatric Genetics, Akdeniz University, Antalya, Turkey
| | - Beyhan Tuysuz
- Department of Pediatrics, Division of Pediatric Genetics, Cerrahpaşa University, Istanbul, Turkey
| | - Esra Isik
- Department of Pediatrics, Division of Pediatric Genetics, Ege University, Izmir, Turkey
| | - Aysegul Yilmaz
- Department of Pediatrics, Division of Pediatric Genetics, Ondokuz Mayıs University, Samsun, Turkey
| | - Yasemin Alanay
- Department of Pediatrics, Division of Pediatric Genetics, Acıbadem University, Istanbul, Turkey
| | - Evrim Cifci Sunamak
- Department of Pediatrics, Division of Pediatric Genetics, Cerrahpaşa University, Istanbul, Turkey
| | | | - Ferda Ozkinay
- Department of Pediatrics, Division of Pediatric Genetics, Ege University, Izmir, Turkey
| | - Gokhan Ozan Cetin
- Department of Medical Genetics, Pamukkale University, Denizli, Turkey
| | - Nuray Ozturk
- Department of Pediatrics, Division of Pediatric Genetics, Akdeniz University, Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatrics, Division of Pediatric Genetics, Akdeniz University, Antalya, Turkey
| | - Banu Nur
- Department of Pediatrics, Division of Pediatric Genetics, Akdeniz University, Antalya, Turkey
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15
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Dong X, Bai Y, Liao Z, Gritsch D, Liu X, Wang T, Borges-Monroy R, Ehrlich A, Serano GE, Feany MB, Beach TG, Scherzer CR. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535194. [PMID: 37066229 PMCID: PMC10103951 DOI: 10.1101/2023.04.01.535194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identified over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1,526 and 3,308 circRNAs were custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 88% of Parkinson's and 80% of Alzheimer's disease-associated genes produced circRNAs. circDNAJC6, produced from a juvenile-onset Parkinson's gene, was already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produced circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA- regulated synaptic specialization in neuropsychiatric diseases.
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Affiliation(s)
- Xianjun Dong
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Genomics and Bioinformatics Hub, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Yunfei Bai
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - David Gritsch
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Xiaoli Liu
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Neurology, Zhejiang Hospital, Zhejiang, China
| | - Tao Wang
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Rebeca Borges-Monroy
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
| | - Alyssa Ehrlich
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mel B. Feany
- Departement of Pathology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Clemens R. Scherzer
- APDA Center for Advanced Parkinson Disease Research, Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, USA
- Precision Neurology Program, Harvard Medical School and Brigham & Women’s Hospital, Boston, MA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA
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16
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Chen S, Neale BM, Berkovic SF. Shared and distinct ultra-rare genetic risk for diverse epilepsies: A whole-exome sequencing study of 54,423 individuals across multiple genetic ancestries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.22.23286310. [PMID: 36865150 PMCID: PMC9980234 DOI: 10.1101/2023.02.22.23286310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Identifying genetic risk factors for highly heterogeneous disorders like epilepsy remains challenging. Here, we present the largest whole-exome sequencing study of epilepsy to date to investigate rare variants that confer risk for a spectrum of epilepsy syndromes. With an unprecedented sample size of >54,000 human exomes, composed of 20,979 deep-phenotyped patients with epilepsy and 33,444 controls, we replicate previous gene findings at exome-wide significance; using a hypothesis-free approach, we identify potential novel associations. Most discoveries are specific to a particular subtype of epilepsy, highlighting distinct genetic contributions to different epilepsies. Combining evidence from rare single nucleotide/short indel-, copy number-, and common variants, we find convergence of different genetic risk factors at the level of individual genes. Further comparing to other exome-sequencing studies, we implicate shared rare variant risk between epilepsy and other neurodevelopmental disorders. Our study also demonstrates the value of collaborative sequencing and deep-phenotyping efforts, which will continue to unravel the complex genetic architecture underlying the heterogeneity of epilepsy.
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Affiliation(s)
- Siwei Chen
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, University of Melbourne, Austin Health, Heidelberg 3084, Australia
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17
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Ford TJL, Jeon BT, Lee H, Kim WY. Dendritic spine and synapse pathology in chromatin modifier-associated autism spectrum disorders and intellectual disability. Front Mol Neurosci 2023; 15:1048713. [PMID: 36743289 PMCID: PMC9892461 DOI: 10.3389/fnmol.2022.1048713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023] Open
Abstract
Formation of dendritic spine and synapse is an essential final step of brain wiring to establish functional communication in the developing brain. Recent findings have displayed altered dendritic spine and synapse morphogenesis, plasticity, and related molecular mechanisms in animal models and post-mortem human brains of autism spectrum disorders (ASD) and intellectual disability (ID). Many genes and proteins are shown to be associated with spines and synapse development, and therefore neurodevelopmental disorders. In this review, however, particular attention will be given to chromatin modifiers such as AT-Rich Interactive Domain 1B (ARID1B), KAT8 regulatory non-specific lethal (NSL) complex subunit 1 (KANSL1), and WD Repeat Domain 5 (WDR5) which are among strong susceptibility factors for ASD and ID. Emerging evidence highlights the critical status of these chromatin remodeling molecules in dendritic spine morphogenesis and synaptic functions. Molecular and cellular insights of ARID1B, KANSL1, and WDR5 will integrate into our current knowledge in understanding and interpreting the pathogenesis of ASD and ID. Modulation of their activities or levels may be an option for potential therapeutic treatment strategies for these neurodevelopmental conditions.
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18
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Pânzaru MC, Popa S, Lupu A, Gavrilovici C, Lupu VV, Gorduza EV. Genetic heterogeneity in corpus callosum agenesis. Front Genet 2022; 13:958570. [PMID: 36246626 PMCID: PMC9562966 DOI: 10.3389/fgene.2022.958570] [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: 05/31/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
The corpus callosum is the largest white matter structure connecting the two cerebral hemispheres. Agenesis of the corpus callosum (ACC), complete or partial, is one of the most common cerebral malformations in humans with a reported incidence ranging between 1.8 per 10,000 livebirths to 230–600 per 10,000 in children and its presence is associated with neurodevelopmental disability. ACC may occur as an isolated anomaly or as a component of a complex disorder, caused by genetic changes, teratogenic exposures or vascular factors. Genetic causes are complex and include complete or partial chromosomal anomalies, autosomal dominant, autosomal recessive or X-linked monogenic disorders, which can be either de novo or inherited. The extreme genetic heterogeneity, illustrated by the large number of syndromes associated with ACC, highlight the underlying complexity of corpus callosum development. ACC is associated with a wide spectrum of clinical manifestations ranging from asymptomatic to neonatal death. The most common features are epilepsy, motor impairment and intellectual disability. The understanding of the genetic heterogeneity of ACC may be essential for the diagnosis, developing early intervention strategies, and informed family planning. This review summarizes our current understanding of the genetic heterogeneity in ACC and discusses latest discoveries.
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Affiliation(s)
- Monica-Cristina Pânzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Setalia Popa
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
- *Correspondence: Setalia Popa, ; Vasile Valeriu Lupu,
| | - Ancuta Lupu
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Cristina Gavrilovici
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Vasile Valeriu Lupu
- Department of Pediatrics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
- *Correspondence: Setalia Popa, ; Vasile Valeriu Lupu,
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
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19
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Agaimy A, Clarke BA, Kolin DL, Lee CH, Lee JC, McCluggage WG, Pöschke P, Stoehr R, Swanson D, Turashvili G, Beckmann MW, Hartmann A, Antonescu CR, Dickson BC. Recurrent KAT6B/A::KANSL1 Fusions Characterize a Potentially Aggressive Uterine Sarcoma Morphologically Overlapping With Low-grade Endometrial Stromal Sarcoma. Am J Surg Pathol 2022; 46:1298-1308. [PMID: 35575789 PMCID: PMC9388494 DOI: 10.1097/pas.0000000000001915] [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] [Indexed: 11/26/2022]
Abstract
With the widespread application of next-generation sequencing, the genetic landscape of uterine mesenchymal neoplasms has been evolving rapidly to include several recently identified fusion genes. Although chromosomal rearrangements involving the 10q22 and 17q21.31 loci have been reported in occasional uterine leiomyomas decades ago, the corresponding KAT6B::KANSL1 fusion has been only recently identified in 2 uterine tumors diagnosed as leiomyoma and leiomyosarcoma. We herein describe 13 uterine stromal neoplasms carrying a KAT6B::KANSL1 (n=11) and KAT6A::KANSL1 (n=2) fusion. Patient ages ranged from 33 to 81 years (median, 49 y). Tumor size was 2.6 to 23.5 cm (median, 8.2 cm). Nine tumors were myometrium-centered, and 3 had an intracavitary component. Original diagnoses were mostly low-grade endometrial stromal sarcoma (LG-ESS; 10 cases) with atypical features (limited CD10 expression, sex cord-like features, pericytic vasculature, and frequent myxoid changes). Treatment was hysterectomy±bilateral salpingo-oophorectomy (10), myomectomy (1), and curettage (2). Five patients were disease-free at 6 to 34 months, 3 (27%) died of disease at 2 to 47 months, and 3 were alive with disease at 2, 17, and 17 years. Histologically, most tumors showed variable overlap with LG-ESS, but they were generally well-circumscribed lacking the extensive permeative and angioinvasive growth typical of LG-ESS. They were composed of monotonous medium-sized oval and spindle cells arranged into diffuse sheets with prominent spiral-type arterioles and frequent pericytoma-like vascular pattern. Variable myxoid stromal changes were frequent. Mitotic activity ranged from 1 to >20 in 10 HPFs. Immunohistochemistry showed variable expression of CD10 (12/13), estrogen receptor (8/11), progesterone receptor (8/11), smooth muscle actin (9/11), desmin (4/12), h-caldesmon (2/10), calretinin (3/8), inhibin (1/7), WT1 (4/7), cyclin D1 (5/11; diffuse in only 1 case), and pankeratin (5/10). This series characterizes a KAT6B/A::KANSL1 fusion-positive uterine stromal neoplasm within the morphologic spectrum of LG-ESS but with atypical features. The relationship of these neoplasms to genuine LG-ESS remains unclear. This molecular subtype of uterine endometrial stromal sarcoma has the potential for an unfavorable clinical course despite the absence of widely invasive growth; nevertheless, analysis of more cases is necessary to delineate the phenotypic spectrum and biological potential of this tumor.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | | | | | | | - Jen-Chieh Lee
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health & Social Care Trust, Belfast, United Kingdom
| | - Patrik Pöschke
- Department of Gynecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Robert Stoehr
- Institute of Pathology, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - David Swanson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Gulisa Turashvili
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Erlangen University Hospital, Comprehensive Cancer Center, European Metropolitan Area Erlangen-Nuremberg (CCC ER-EMN), Friedrich Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
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20
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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21
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Deng Z, Zhou X, Lu JH, Yue Z. Autophagy deficiency in neurodevelopmental disorders. Cell Biosci 2021; 11:214. [PMID: 34920755 PMCID: PMC8684077 DOI: 10.1186/s13578-021-00726-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 12/27/2022] Open
Abstract
Autophagy is a cell self-digestion pathway through lysosome and plays a critical role in maintaining cellular homeostasis and cytoprotection. Characterization of autophagy related genes in cell and animal models reveals diverse physiological functions of autophagy in various cell types and tissues. In central nervous system, by recycling injured organelles and misfolded protein complexes or aggregates, autophagy is integrated into synaptic functions of neurons and subjected to distinct regulation in presynaptic and postsynaptic neuronal compartments. A plethora of studies have shown the neuroprotective function of autophagy in major neurodegenerative diseases, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD) and amyotrophic lateral sclerosis (ALS). Recent human genetic and genomic evidence has demonstrated an emerging, significant role of autophagy in human brain development and prevention of spectrum of neurodevelopmental disorders. Here we will review the evidence demonstrating the causal link of autophagy deficiency to congenital brain diseases, the mechanism whereby autophagy functions in neurodevelopment, and therapeutic potential of autophagy.
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Affiliation(s)
- Zhiqiang Deng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Xiaoting Zhou
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jia-Hong Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China.
| | - Zhenyu Yue
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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22
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Mir US, Bhat A, Mushtaq A, Pandita S, Altaf M, Pandita TK. Role of histone acetyltransferases MOF and Tip60 in genome stability. DNA Repair (Amst) 2021; 107:103205. [PMID: 34399315 DOI: 10.1016/j.dnarep.2021.103205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 01/23/2023]
Abstract
The accurate repair of DNA damage specifically the chromosomal double-strand breaks (DSBs) arising from exposure to physical or chemical agents, such as ionizing radiation (IR) and radiomimetic drugs is critical in maintaining genomic integrity. The DNA DSB response and repair is facilitated by hierarchical signaling networks that orchestrate chromatin structural changes specifically histone modifications which impact cell-cycle checkpoints through enzymatic activities to repair the broken DNA ends. Various histone posttranslational modifications such as phosphorylation, acetylation, methylation and ubiquitylation have been shown to play a role in DNA damage repair. Recent studies have provided important insights into the role of histone-specific modifications in sensing DNA damage and facilitating the DNA repair. Histone modifications have been shown to determine the pathway choice for repair of DNA DSBs. This review will summarize the role of important histone acetyltransferases MOF and Tip60 mediated acetylation in repair of DNA DSBs in eukaryotic cells.
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Affiliation(s)
- Ulfat Syed Mir
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, 181143, India
| | - Arjamand Mushtaq
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Shruti Pandita
- Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Mohammad Altaf
- Chromatin and Epigenetics Lab, Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India; Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
| | - Tej K Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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23
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Farnè M, Bernardini L, Capalbo A, Cavarretta G, Torres B, Sanchini M, Fini S, Ferlini A, Bigoni S. Koolen-de Vries syndrome in a 63-year-old woman: Report of the oldest patient and a review of the adult phenotype. Am J Med Genet A 2021; 188:692-707. [PMID: 34665525 PMCID: PMC9297928 DOI: 10.1002/ajmg.a.62536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022]
Abstract
Koolen-de Vries syndrome (KdVS) is a rare genetic disorder caused by a de novo microdeletion in chromosomal region 17q21.31 encompassing KANSL1 or by a de novo intragenic pathogenic variant of KANSL1. KdVS is typically characterized by intellectual disability (ID), variable from mild to severe, developmental psychomotor delay, especially of expressive language development, friendly disposition, and multiple systemic abnormalities. So far, most of the individuals affected by KdVS are diagnosed in infancy or in adolescence; to the best of our knowledge, only 34 (including ours) adults have been reported in literature. Here we present the adult phenotype of a 63-year-old Italian woman affected by KdVS, caused by a 17q21.31 microdeletion. She is, to our knowledge, the oldest affected individual reported so far. We collected her clinical history and photographs, as well as those of other 26 adult patients described so far and compared her to them. We propose that the cardinal features of KdVS in adulthood are ID (ranging from mild to severe, usually moderate), friendly behavior, musculoskeletal abnormalities (especially scoliosis), and facial dysmorphism (a long face and a pronounced pear-shape nose with bulbous overhanging nasal tip). Therefore, we suggest considering KdVS in differential diagnosis in adult patients characterized by these features.
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Affiliation(s)
- Marianna Farnè
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Laura Bernardini
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo (FG), Italy
| | - Anna Capalbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo (FG), Italy
| | - Giusy Cavarretta
- Medical Genetics Unit, Department of Mother and Child, Ferrara Sant'Anna University Hospital, Ferrara, Italy
| | - Barbara Torres
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo (FG), Italy
| | - Mariabeatrice Sanchini
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Sergio Fini
- Medical Genetics Unit, Department of Mother and Child, Ferrara Sant'Anna University Hospital, Ferrara, Italy
| | - Alessandra Ferlini
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy.,Medical Genetics Unit, Department of Mother and Child, Ferrara Sant'Anna University Hospital, Ferrara, Italy
| | - Stefania Bigoni
- Medical Genetics Unit, Department of Mother and Child, Ferrara Sant'Anna University Hospital, Ferrara, Italy
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24
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Leveille E, Ross OA, Gan-Or Z. Tau and MAPT genetics in tauopathies and synucleinopathies. Parkinsonism Relat Disord 2021; 90:142-154. [PMID: 34593302 DOI: 10.1016/j.parkreldis.2021.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
MAPT encodes the microtubule-associated protein tau, which is the main component of neurofibrillary tangles (NFTs) and found in other protein aggregates. These aggregates are among the pathological hallmarks of primary tauopathies such as frontotemporal dementia (FTD). Abnormal tau can also be observed in secondary tauopathies such as Alzheimer's disease (AD) and synucleinopathies such as Parkinson's disease (PD). On top of pathological findings, genetic data also links MAPT to these disorders. MAPT variations are a cause or risk factors for many tauopathies and synucleinopathies and are associated with certain clinical and pathological features in affected individuals. In addition to clinical, pathological, and genetic overlap, evidence also suggests that tau and alpha-synuclein may interact on the molecular level, and thus might collaborate in the neurodegenerative process. Understanding the role of MAPT variations in tauopathies and synucleinopathies is therefore essential to elucidate the role of tau in the pathogenesis and phenotype of those disorders, and ultimately to develop targeted therapies. In this review, we describe the role of MAPT genetic variations in tauopathies and synucleinopathies, several genotype-phenotype and pathological features, and discuss their implications for the classification and treatment of those disorders.
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Affiliation(s)
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA; Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-hospital), McGill University, Montréal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada; Department of Human Genetics, McGill University, Montréal, QC, Canada.
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25
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Burger P, Coutelle R, Strehle A, Colin F, Collot N, Koolen D, Kleefstra T, Mandel JL. GenIDA : l’histoire naturelle et les comorbidités des troubles du neurodéveloppement d’origine génétique. ENFANCE 2021. [DOI: 10.3917/enf2.213.0229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Linda K, Lewerissa EI, Verboven AHA, Gabriele M, Frega M, Klein Gunnewiek TM, Devilee L, Ulferts E, Hommersom M, Oudakker A, Schoenmaker C, van Bokhoven H, Schubert D, Testa G, Koolen DA, de Vries BBA, Nadif Kasri N. Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders. Autophagy 2021; 18:423-442. [PMID: 34286667 PMCID: PMC8942553 DOI: 10.1080/15548627.2021.1936777] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Macroautophagy (hereafter referred to as autophagy) is a finely tuned process of programmed degradation and recycling of proteins and cellular components, which is crucial in neuronal function and synaptic integrity. Mounting evidence implicates chromatin remodeling in fine-tuning autophagy pathways. However, this epigenetic regulation is poorly understood in neurons. Here, we investigate the role in autophagy of KANSL1, a member of the nonspecific lethal complex, which acetylates histone H4 on lysine 16 (H4K16ac) to facilitate transcriptional activation. Loss-of-function of KANSL1 is strongly associated with the neurodevelopmental disorder Koolen-de Vries Syndrome (KdVS). Starting from KANSL1-deficient human induced-pluripotent stem cells, both from KdVS patients and genome-edited lines, we identified SOD1 (superoxide dismutase 1), an antioxidant enzyme, to be significantly decreased, leading to a subsequent increase in oxidative stress and autophagosome accumulation. In KANSL1-deficient neurons, autophagosome accumulation at excitatory synapses resulted in reduced synaptic density, reduced GRIA/AMPA receptor-mediated transmission and impaired neuronal network activity. Furthermore, we found that increased oxidative stress-mediated autophagosome accumulation leads to increased MTOR activation and decreased lysosome function, further preventing the clearing of autophagosomes. Finally, by pharmacologically reducing oxidative stress, we could rescue the aberrant autophagosome formation as well as synaptic and neuronal network activity in KANSL1-deficient neurons. Our findings thus point toward an important relation between oxidative stress-induced autophagy and synapse function, and demonstrate the importance of H4K16ac-mediated changes in chromatin structure to balance reactive oxygen species- and MTOR-dependent autophagy. Abbreviations: APO: apocynin; ATG: autophagy related; BAF: bafilomycin A1; BSO: buthionine sulfoximine; CV: coefficient of variation; DIV: days in vitro; H4K16ac: histone 4 lysine 16 acetylation; iPSC: induced-pluripotent stem cell; KANSL1: KAT8 regulatory NSL complex subunit 1; KdVS: Koolen-de Vries Syndrome; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEA: micro-electrode array; MTOR: mechanistic target of rapamycin kinase; NSL complex: nonspecific lethal complex; 8-oxo-dG: 8-hydroxydesoxyguanosine; RAP: rapamycin; ROS: reactive oxygen species; sEPSCs: spontaneous excitatory postsynaptic currents; SOD1: superoxide dismutase 1; SQSTM1/p62: sequestosome 1; SYN: synapsin; WRT: wortmannin.
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Affiliation(s)
- Katrin Linda
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Elly I Lewerissa
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Anouk H A Verboven
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Michele Gabriele
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy.,Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Monica Frega
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands.,Department of Clinical Neurophysiology, University of Twente, Enschede, The Netherlands
| | - Teun M Klein Gunnewiek
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands.,Department of Anatomy, Radboudumc, Donders Institute for Brain, Cognition, and Behaviour, Nijmegen, The Netherlands
| | - Lynn Devilee
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Edda Ulferts
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Marina Hommersom
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Astrid Oudakker
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Chantal Schoenmaker
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Giuseppe Testa
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy.,Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - David A Koolen
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
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27
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Antonarakis SE. History of the methodology of disease gene identification. Am J Med Genet A 2021; 185:3266-3275. [PMID: 34159713 PMCID: PMC8596769 DOI: 10.1002/ajmg.a.62400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/06/2022]
Abstract
The past 45 years have witnessed a triumph in the discovery of genes and genetic variation that cause Mendelian disorders due to high impact variants. Important discoveries and organized projects have provided the necessary tools and infrastructure for the identification of gene defects leading to thousands of monogenic phenotypes. This endeavor can be divided in three phases in which different laboratory strategies were employed for the discovery of disease-related genes: (i) the biochemical phase, (ii) the genetic linkage followed by positional cloning phase, and (iii) the sequence identification phase. However, much more work is needed to identify all the high impact genomic variation that substantially contributes to the phenotypic variation.
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Affiliation(s)
- Stylianos E Antonarakis
- University of Geneva Medical School, Geneva, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
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28
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Krude H, Mundlos S, Øien NC, Opitz R, Schuelke M. What can go wrong in the non-coding genome and how to interpret whole genome sequencing data. MED GENET-BERLIN 2021; 33:121-131. [PMID: 38836035 PMCID: PMC11007630 DOI: 10.1515/medgen-2021-2071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/24/2021] [Indexed: 06/06/2024]
Abstract
Whole exome sequencing discovers causative mutations in less than 50 % of rare disease patients, suggesting the presence of additional mutations in the non-coding genome. So far, non-coding mutations have been identified in less than 0.2 % of individuals with genetic diseases listed in the ClinVar database and exhibit highly diverse molecular mechanisms. In contrast to our capability to sequence the whole genome, our ability to discover and functionally confirm such non-coding mutations is lagging behind severely. We discuss the problems and present examples of confirmed mutations in deep intronic sequences, non-coding triplet repeats, enhancers, and larger structural variants and highlight their proposed disease mechanisms. Finally, we discuss the type of data that would be required to establish non-coding mutation detection in routine diagnostics.
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Affiliation(s)
- Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nancy Christine Øien
- Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robert Opitz
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus Schuelke
- Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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29
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García-Santiago FA, Martínez-Payo C, Mansilla E, Santos-Simarro F, Ruiz de Azua Ballesteros M, Mori MÁ, Antolín Alvarado E, Nieto Y, Vallcorba I, Tenorio J, Nevado J, Lapunzina P. Prenatal ultrasound findings in Koolen-de Vries foetuses: Central nervous system anomalies are frequent markers of this syndrome. Mol Genet Genomic Med 2021; 9:e1649. [PMID: 33733630 PMCID: PMC8172212 DOI: 10.1002/mgg3.1649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 11/12/2022] Open
Abstract
Objective Prenatal diagnoses of microdeletion syndromes without ultrasound findings in the first and second trimester are always difficult. The objective of this study is to report the prenatal ultrasound findings in four foetuses diagnosed with 17q21.31 microdeletions (Koolen‐de Vries syndrome) using chromosomal microarrays (CMA). Patients and Methods We present four foetuses with 17q21.31 microdeletion. All showed CNS anomalies in the third trimester, three had ventriculomegaly, and one hypogenesis of corpus callosum at 31 weeks of pregnancy. Results Array‐SNPs and CGH‐array were performed on uncultured amniocytes and peripheral blood revealing a 17q21.31 microdeletion. Conclusions Prenatal CNS anomalies (mainly ventriculomegaly) at third trimester, in spite of isolate, should be considered a prenatal ultrasound marker of this syndrome. This kind of malformations raise the possibility of an underlying genetic conditions including 17q21.31 microdeletion; thus, CMA should be taken into consideration when offering prenatal genetic counselling.
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Affiliation(s)
- Fe Amalia García-Santiago
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 753, ISCIII, Madrid, Spain.,The European Reference Network on Intellectual Disability, TeleHealth and Congenital Anomalies (ERN ITHACA), Brussels, Belgium
| | - Cristina Martínez-Payo
- Department of Gynecology and Obstetrics, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Elena Mansilla
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 753, ISCIII, Madrid, Spain.,The European Reference Network on Intellectual Disability, TeleHealth and Congenital Anomalies (ERN ITHACA), Brussels, Belgium
| | - Fernando Santos-Simarro
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 753, ISCIII, Madrid, Spain.,The European Reference Network on Intellectual Disability, TeleHealth and Congenital Anomalies (ERN ITHACA), Brussels, Belgium
| | | | - María Ángeles Mori
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 753, ISCIII, Madrid, Spain
| | - Eugenia Antolín Alvarado
- Universidad Autónoma de Madrid, Madrid, Spain.,Department of Gynecology and Obstetrics, Hospital Universitario La Paz, Madrid, Spain
| | - Yolanda Nieto
- Department of Gynecology and Obstetrics, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Isabel Vallcorba
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Jair Tenorio
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 753, ISCIII, Madrid, Spain.,The European Reference Network on Intellectual Disability, TeleHealth and Congenital Anomalies (ERN ITHACA), Brussels, Belgium
| | - Julián Nevado
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 753, ISCIII, Madrid, Spain.,The European Reference Network on Intellectual Disability, TeleHealth and Congenital Anomalies (ERN ITHACA), Brussels, Belgium
| | - Pablo Lapunzina
- INGEMM, Institute of Medical and Molecular Genetics-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Unidad 753, ISCIII, Madrid, Spain.,The European Reference Network on Intellectual Disability, TeleHealth and Congenital Anomalies (ERN ITHACA), Brussels, Belgium
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30
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Chang CW, Shao E, Mucke L. Tau: Enabler of diverse brain disorders and target of rapidly evolving therapeutic strategies. Science 2021; 371:371/6532/eabb8255. [PMID: 33632820 DOI: 10.1126/science.abb8255] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Several lines of evidence implicate the protein tau in the pathogenesis of multiple brain disorders, including Alzheimer's disease, other neurodegenerative conditions, autism, and epilepsy. Tau is abundant in neurons and interacts with microtubules, but its main functions in the brain remain to be defined. These functions may involve the regulation of signaling pathways relevant to diverse biological processes. Informative disease models have revealed a plethora of abnormal tau species and mechanisms that might contribute to neuronal dysfunction and loss, but the relative importance of their respective contributions is uncertain. This knowledge gap poses major obstacles to the development of truly impactful therapeutic strategies. The current expansion and intensification of efforts to translate mechanistic insights into tau-related therapeutics should address this issue and could deliver better treatments for a host of devastating conditions.
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Affiliation(s)
- Che-Wei Chang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Eric Shao
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA. .,Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
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31
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Saxena D, Moirangthem A, Shambhavi A, Phadke SR. Koolen‐de Vries syndrome: First report of two unrelated Indian patients. Am J Med Genet A 2021. [DOI: 10.1002/ajmg.a.62008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Deepti Saxena
- Department of Medical Genetics Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow India
| | - Amita Moirangthem
- Department of Medical Genetics Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow India
| | - Arya Shambhavi
- Department of Medical Genetics Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow India
| | - Shubha R. Phadke
- Department of Medical Genetics Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow India
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32
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Quantitative facial phenotyping for Koolen-de Vries and 22q11.2 deletion syndrome. Eur J Hum Genet 2021; 29:1418-1423. [PMID: 33603161 DOI: 10.1038/s41431-021-00824-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/21/2020] [Accepted: 01/26/2021] [Indexed: 01/08/2023] Open
Abstract
The Koolen-de Vries syndrome (KdVS) is a multisystem syndrome with variable facial features caused by a 17q21.31 microdeletion or KANSL1 truncating variant. As the facial gestalt of KdVS has resemblance with the gestalt of the 22q11.2 deletion syndrome (22q11.2DS), we assessed whether our previously described hybrid quantitative facial phenotyping algorithm could distinguish between these two syndromes, and whether there is a facial difference between the molecular KdVS subtypes. We applied our algorithm to 2D photographs of 97 patients with KdVS (78 microdeletions, 19 truncating variants (likely) causing KdVS) and 48 patients with 22q11.2DS as well as age, gender and ethnicity matched controls with intellectual disability (n = 145). The facial gestalts of KdVS and 22q11.2DS were both recognisable through significant clustering by the hybrid model, yet different from one another (p = 7.5 × 10-10 and p = 0.0052, respectively). Furthermore, the facial gestalts of KdVS caused by a 17q21.31 microdeletion and KANSL1 truncating variant (likely) causing KdVS were indistinguishable (p = 0.981 and p = 0.130). Further application to three patients with a variant of unknown significance in KANSL1 showed that these faces do not match KdVS. Our data highlight quantitative facial phenotyping not only as a powerful tool to distinguish syndromes with overlapping facial dysmorphisms but also to establish pathogenicity of variants of unknown clinical significance.
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33
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Dingemans AJM, Stremmelaar DE, Vissers LELM, Jansen S, Nabais Sá MJ, van Remortele A, Jonis N, Truijen K, van de Ven S, Ewals J, Verbruggen M, Koolen DA, Brunner HG, Eichler EE, Gecz J, de Vries BBA. Human disease genes website series: An international, open and dynamic library for up-to-date clinical information. Am J Med Genet A 2021; 185:1039-1046. [PMID: 33439542 PMCID: PMC7986414 DOI: 10.1002/ajmg.a.62057] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/11/2022]
Abstract
Since the introduction of next‐generation sequencing, an increasing number of disorders have been discovered to have genetic etiology. To address diverse clinical questions and coordinate research activities that arise with the identification of these rare disorders, we developed the Human Disease Genes website series (HDG website series): an international digital library that records detailed information on the clinical phenotype of novel genetic variants in the human genome (https://humandiseasegenes.info/). Each gene website is moderated by a dedicated team of clinicians and researchers, focused on specific genes, and provides up‐to‐date—including unpublished—clinical information. The HDG website series is expanding rapidly with 424 genes currently adopted by 325 moderators from across the globe. On average, a gene website has detailed phenotypic information of 14.4 patients. There are multiple examples of added value, one being the ARID1B gene website, which was recently utilized in research to collect clinical information of 81 new patients. Additionally, several gene websites have more data available than currently published in the literature. In conclusion, the HDG website series provides an easily accessible, open and up‐to‐date clinical data resource for patients with pathogenic variants of individual genes. This is a valuable resource not only for clinicians dealing with rare genetic disorders such as developmental delay and autism, but other professionals working in diagnostics and basic research. Since the HDG website series is a dynamic platform, its data also include the phenotype of yet unpublished patients curated by professionals providing higher quality clinical detail to improve management of these rare disorders.
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Affiliation(s)
- Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Diante E Stremmelaar
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Maria J Nabais Sá
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Angela van Remortele
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Noraly Jonis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Kim Truijen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Sam van de Ven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Jeroen Ewals
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Michel Verbruggen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
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34
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Amenta S, Frangella S, Marangi G, Lattante S, Ricciardi S, Doronzio PN, Orteschi D, Veredice C, Contaldo I, Zampino G, Gentile M, Scarano E, Graziano C, Zollino M. Adult phenotype in Koolen-de Vries/ KANSL1 haploinsufficiency syndrome. J Med Genet 2020; 59:189-195. [PMID: 33361104 DOI: 10.1136/jmedgenet-2020-107225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/02/2020] [Accepted: 11/26/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND Koolen-de Vries syndrome (KdVS) is a multisystem neurodevelopmental disorder caused by 17q21.31 deletions or mutations in KANSL1. It was mainly described in children. METHODS A retrospective study on 9 subjects aged 19-45 years and revision of 18 literature patients, with the purpose to get insights into the phenotypic evolution with time, and into the clinical manifestations in adulthood. RESULTS Seven patients had a 17q21.31 deletion and two a point mutation in KANSL1. All had intellectual disability, which was mild in five (56%) and moderate in four (44%). Epilepsy was diagnosed in four subjects (44%), with onset from 1 to 7 years and full remission before 9 years in 3/4 patients. Scoliosis affected seven individuals (77.7%) and it was substantially stable with age in 5/7 patients, allowing for simple daily activities. Two subjects had severely progressive scoliosis, which was surgically corrected. Overweight or true obesity did occur after puberty in six patients (67%). Behaviour abnormalities were recorded in six patients (67%). The facial phenotype slightly evolved with time to include thick eyebrows, elongated nose and pronounced pointed chin. Despite behaviour abnormalities, happy disposition and sociable attitudes were common. Half of patients had fluent language and were good at writing and reading. Rich language, although limited to single words or short sentences, and very limited or absent skills in writing and reading were observed in the remaining patients. Autonomy in daily activities and personal care was usually limited. CONCLUSIONS Distinctive features in adult KdVS subjects include intellectual disability, overweight/obesity, behaviour abnormalities with preserved social interest, ability in language, slight worsening of the facial phenotype and no seizures.
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Affiliation(s)
- Simona Amenta
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Roma, Italy
| | - Silvia Frangella
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Roma, Italy
| | - Giuseppe Marangi
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Roma, Italy.,Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Serena Lattante
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Roma, Italy.,Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Stefania Ricciardi
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Roma, Italy
| | - Paolo Niccolò Doronzio
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Roma, Italy
| | - Daniela Orteschi
- Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Chiara Veredice
- Neuropsichiatria Infantile, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Ilaria Contaldo
- Neuropsichiatria Infantile, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Giuseppe Zampino
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Pediatria, Università Cattolica Sacro Cuore, Facoltà di Medicina e Chirurgia, Roma, Italy.,Pediatria, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Mattia Gentile
- Genetica Medica, Dipartimento Materno-Infantile, Ospedale di Venere, Bari, Italy
| | - Emanuela Scarano
- Dipartimento di Pediatria, Policlinico Universitario S. Orsola, Bologna, Italy
| | - Claudio Graziano
- Genetica Medica, Università di Bologna, Dipartimento Scienze Ginecologiche, Ostetriche e Pediatriche, Bologna, Italy
| | - Marcella Zollino
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Roma, Italy .,Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
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35
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Li L, Ghorbani M, Weisz-Hubshman M, Rousseau J, Thiffault I, Schnur RE, Breen C, Oegema R, Weiss MM, Waisfisz Q, Welner S, Kingston H, Hills JA, Boon EM, Basel-Salmon L, Konen O, Goldberg-Stern H, Bazak L, Tzur S, Jin J, Bi X, Bruccoleri M, McWalter K, Cho MT, Scarano M, Schaefer GB, Brooks SS, Hughes SS, van Gassen KLI, van Hagen JM, Pandita TK, Agrawal PB, Campeau PM, Yang XJ. Lysine acetyltransferase 8 is involved in cerebral development and syndromic intellectual disability. J Clin Invest 2020; 130:1431-1445. [PMID: 31794431 DOI: 10.1172/jci131145] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/21/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic integrity is critical for many eukaryotic cellular processes. An important question is how different epigenetic regulators control development and influence disease. Lysine acetyltransferase 8 (KAT8) is critical for acetylation of histone H4 at lysine 16 (H4K16), an evolutionarily conserved epigenetic mark. It is unclear what roles KAT8 plays in cerebral development and human disease. Here, we report that cerebrum-specific knockout mice displayed cerebral hypoplasia in the neocortex and hippocampus, along with improper neural stem and progenitor cell (NSPC) development. Mutant cerebrocortical neuroepithelia exhibited faulty proliferation, aberrant neurogenesis, massive apoptosis, and scant H4K16 propionylation. Mutant NSPCs formed poor neurospheres, and pharmacological KAT8 inhibition abolished neurosphere formation. Moreover, we describe KAT8 variants in 9 patients with intellectual disability, seizures, autism, dysmorphisms, and other anomalies. The variants altered chromobarrel and catalytic domains of KAT8, thereby impairing nucleosomal H4K16 acetylation. Valproate was effective for treating epilepsy in at least 2 of the individuals. This study uncovers a critical role of KAT8 in cerebral and NSPC development, identifies 9 individuals with KAT8 variants, and links deficient H4K16 acylation directly to intellectual disability, epilepsy, and other developmental anomalies.
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Affiliation(s)
- Lin Li
- Rosalind and Morris Goodman Cancer Research Centre and Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Mohammad Ghorbani
- Rosalind and Morris Goodman Cancer Research Centre and Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Monika Weisz-Hubshman
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Justine Rousseau
- Paediatric Department, CHU Sainte-Justine Hospital, University of Montreal, Quebec, Canada
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine & Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,Faculty of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Rhonda E Schnur
- Division of Genetics, Cooper University Health Care, Camden, New Jersey, USA.,GeneDx, Gaithersburg, Maryland, USA
| | - Catherine Breen
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, United Kingdom
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marjan Mm Weiss
- Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Sara Welner
- Division of Pediatric Medical Genetics, The State University of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Helen Kingston
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, United Kingdom
| | - Jordan A Hills
- University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Elles Mj Boon
- Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Lina Basel-Salmon
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petach Tikva, Israel
| | - Osnat Konen
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Imaging Department, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Hadassa Goldberg-Stern
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Epilepsy Unit and EEG Laboratory, Schneider Medical Center, Petach Tikva, Israel
| | - Lily Bazak
- Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shay Tzur
- Laboratory of Molecular Medicine, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel.,Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel
| | - Jianliang Jin
- Rosalind and Morris Goodman Cancer Research Centre and Department of Medicine, McGill University, Montreal, Quebec, Canada.,Research Center for Bone and Stem Cells, Department of Human Anatomy, Key Laboratory of Aging & Disease, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiuli Bi
- Rosalind and Morris Goodman Cancer Research Centre and Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Michael Bruccoleri
- Rosalind and Morris Goodman Cancer Research Centre and Department of Medicine, McGill University, Montreal, Quebec, Canada
| | | | | | - Maria Scarano
- Division of Genetics, Cooper University Health Care, Camden, New Jersey, USA
| | | | - Susan S Brooks
- Division of Pediatric Medical Genetics, The State University of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Susan Starling Hughes
- Center for Pediatric Genomic Medicine & Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,Faculty of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - K L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas, USA
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Philippe M Campeau
- Paediatric Department, CHU Sainte-Justine Hospital, University of Montreal, Quebec, Canada
| | - Xiang-Jiao Yang
- Rosalind and Morris Goodman Cancer Research Centre and Department of Medicine, McGill University, Montreal, Quebec, Canada.,Departments of Biochemistry and Medicine, McGill University Health Center, Montreal, Quebec, Canada
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Clinical Genetics Can Solve the Pitfalls of Genome-Wide Investigations: Lesson from Mismapping a Loss-of-Function Variant in KANSL1. Genes (Basel) 2020; 11:genes11101177. [PMID: 33050294 PMCID: PMC7600039 DOI: 10.3390/genes11101177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
Massive parallel sequencing of 70 genes in a girl with a suspicion of chromatinopathy detected the (NM_015443.4:)c.985_986delTT variant in exon 2 of KANSL1, which led to a diagnostic consideration of Koolen De Vries syndrome. The same variant was present in the healthy mother, consistent with either incomplete penetrance or variant mismapping. A network of second opinion was implemented among clinical geneticists first, and a diagnosis of Koolen De Vries syndrome was considered unlikely. By MLPA, a duplication spanning exons 1-3 of KANSL1 was detected in both the mother and the daughter. On cDNA sequencing, biallelic wild type mRNA was observed. We concluded that the variant affects the noncoding duplicated gene region in our family, and we finally classified it as benign. Parallel wide genomic sequencing is increasingly the first genetic investigation in individuals with intellectual disability. The c.985_986delTT variant in KANSL1 was described both in individuals with typical KdVS and in a limited number of healthy subjects. This report highlights the role of clinical genetics to correctly classify variants and to define proper clinical and diagnostic correlations.
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Brain-Enriched Coding and Long Non-coding RNA Genes Are Overrepresented in Recurrent Neurodevelopmental Disorder CNVs. Cell Rep 2020; 33:108307. [PMID: 33113368 DOI: 10.1016/j.celrep.2020.108307] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/15/2020] [Accepted: 10/02/2020] [Indexed: 11/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition with substantial phenotypic and etiological heterogeneity. Although 10%-20% of ASD cases are attributable to copy number variation (CNV), causative genomic loci and constituent genes remain unclarified. We have developed SNATCNV, a tool that outperforms existing tools, to identify 47 recurrent ASD CNV regions from 19,663 cases and 6,479 controls documented in the AutDB database. Analysis of ASD CNV gene content using FANTOM5 shows that constituent coding genes and long non-coding RNAs have brain-enriched patterns of expression. Notably, such enrichment is not observed for regions identified by using other tools. We also find evidence of sexual dimorphism, one locus uniquely comprising a single lncRNA gene, and correlation of CNVs to distinct clinical and behavioral traits. Finally, we analyze a large dataset for schizophrenia to further demonstrate that SNATCNV is an effective, publicly available tool to define genomic loci and causative genes for multiple CNV-associated conditions.
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The genetic architecture of human brainstem structures and their involvement in common brain disorders. Nat Commun 2020; 11:4016. [PMID: 32782260 PMCID: PMC7421944 DOI: 10.1038/s41467-020-17376-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Brainstem regions support vital bodily functions, yet their genetic architectures and involvement in common brain disorders remain understudied. Here, using imaging-genetics data from a discovery sample of 27,034 individuals, we identify 45 brainstem-associated genetic loci, including the first linked to midbrain, pons, and medulla oblongata volumes, and map them to 305 genes. In a replication sample of 7432 participants most of the loci show the same effect direction and are significant at a nominal threshold. We detect genetic overlap between brainstem volumes and eight psychiatric and neurological disorders. In additional clinical data from 5062 individuals with common brain disorders and 11,257 healthy controls, we observe differential volume alterations in schizophrenia, bipolar disorder, multiple sclerosis, mild cognitive impairment, dementia, and Parkinson’s disease, supporting the relevance of brainstem regions and their genetic architectures in common brain disorders. The genetic architecture underlying brainstem regions and how this links to common brain disorders is not well understood. Here, the authors use MRI and GWAS data from 27,034 individuals to identify genetic and morphological brainstem features that influence common brain disorders.
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard D, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Werge T, Nordentoft M. Quantitative genome-wide association analyses of receptive language in the Danish High Risk and Resilience Study. BMC Neurosci 2020; 21:30. [PMID: 32635940 PMCID: PMC7341668 DOI: 10.1186/s12868-020-00581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND One of the most basic human traits is language. Linguistic ability, and disability, have been shown to have a strong genetic component in family and twin studies, but molecular genetic studies of language phenotypes are scarce, relative to studies of other cognitive traits and neurodevelopmental phenotypes. Moreover, most genetic studies examining such phenotypes do not incorporate parent-of-origin effects, which could account for some of the heritability of the investigated trait. We performed a genome-wide association study of receptive language, examining both child genetic effects and parent-of-origin effects. RESULTS Using a family-based cohort with 400 children with receptive language scores, we found a genome-wide significant paternal parent-of-origin effect with a SNP, rs11787922, on chromosome 9q21.31, whereby the T allele reduced the mean receptive language score by ~ 23, constituting a reduction of more than 1.5 times the population SD (P = 1.04 × 10-8). We further confirmed that this association was not driven by broader neurodevelopmental diagnoses in the child or a family history of psychiatric diagnoses by incorporating covariates for the above and repeating the analysis. CONCLUSIONS Our study reports a genome-wide significant association for receptive language skills; to our knowledge, this is the first documented genome-wide significant association for this phenotype. Furthermore, our study illustrates the importance of considering parent-of-origin effects in association studies, particularly in the case of cognitive or neurodevelopmental traits, in which parental genetic data are not always incorporated.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Section for Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Nicoline Hemager
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Birgitte K Burton
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Aja N Greve
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Richardt M Jepsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
- Center for Neuropsychiatric Schizophrenia Research and Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Anne A E Thorup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Mental Health Centre for Child and Adolescent Psychiatry-Research unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark.
- Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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López-Tobón A, Trattaro S, Testa G. The sociability spectrum: evidence from reciprocal genetic copy number variations. Mol Autism 2020; 11:50. [PMID: 32546261 PMCID: PMC7298749 DOI: 10.1186/s13229-020-00347-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/11/2020] [Indexed: 02/14/2023] Open
Abstract
Sociability entails some of the most complex behaviors processed by the central nervous system. It includes the detection, integration, and interpretation of social cues and elaboration of context-specific responses that are quintessentially species-specific. There is an ever-growing accumulation of molecular associations to autism spectrum disorders (ASD), from causative genes to endophenotypes across multiple functional layers; these however, have rarely been put in context with the opposite manifestation featured in hypersociability syndromes. Genetic copy number variations (CNVs) allow to investigate the relationships between gene dosage and its corresponding phenotypes. In particular, CNVs of the 7q11.23 locus, which manifest diametrically opposite social behaviors, offer a privileged window to look into the molecular substrates underlying the developmental trajectories of the social brain. As by definition sociability is studied in humans postnatally, the developmental fluctuations causing social impairments have thus far remained a black box. Here, we review key evidence of molecular players involved at both ends of the sociability spectrum, focusing on genetic and functional associations of neuroendocrine regulators and synaptic transmission pathways. We then proceed to propose the existence of a molecular axis centered around the paradigmatic dosage imbalances at the 7q11.23 locus, regulating networks responsible for the development of social behavior in humans and highlight the key role that neurodevelopmental models from reprogrammed pluripotent cells will play for its understanding.
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Affiliation(s)
- Alejandro López-Tobón
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
| | - Sebastiano Trattaro
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy.
- Department of Oncology and Hemato-oncology, Università degli studi di Milano, Milan, Italy.
- Human Technopole, Via Cristina Belgioioso 171, Milan, Italy.
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Neural metabolic imbalance induced by MOF dysfunction triggers pericyte activation and breakdown of vasculature. Nat Cell Biol 2020; 22:828-841. [PMID: 32541879 DOI: 10.1038/s41556-020-0526-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Mutations in chromatin-modifying complexes and metabolic enzymes commonly underlie complex human developmental syndromes affecting multiple organs. A major challenge is to determine how disease-causing genetic lesions cause deregulation of homeostasis in unique cell types. Here we show that neural-specific depletion of three members of the non-specific lethal (NSL) chromatin complex-Mof, Kansl2 or Kansl3-unexpectedly leads to severe vascular defects and brain haemorrhaging. Deregulation of the epigenetic landscape induced by the loss of the NSL complex in neural cells causes widespread metabolic defects, including an accumulation of free long-chain fatty acids (LCFAs). Free LCFAs induce a Toll-like receptor 4 (TLR4)-NFκB-dependent pro-inflammatory signalling cascade in neighbouring vascular pericytes that is rescued by TLR4 inhibition. Pericytes display functional changes in response to LCFA-induced activation that result in vascular breakdown. Our work establishes that neurovascular function is determined by the neural metabolic environment.
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42
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Gaub A, Sheikh BN, Basilicata MF, Vincent M, Nizon M, Colson C, Bird MJ, Bradner JE, Thevenon J, Boutros M, Akhtar A. Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation. Nat Commun 2020; 11:2243. [PMID: 32382029 PMCID: PMC7206058 DOI: 10.1038/s41467-020-16103-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Cells rely on a diverse repertoire of genes for maintaining homeostasis, but the transcriptional networks underlying their expression remain poorly understood. The MOF acetyltransferase-containing Non-Specific Lethal (NSL) complex is a broad transcription regulator. It is essential in Drosophila, and haploinsufficiency of the human KANSL1 subunit results in the Koolen-de Vries syndrome. Here, we perform a genome-wide RNAi screen and identify the BET protein BRD4 as an evolutionary conserved co-factor of the NSL complex. Using Drosophila and mouse embryonic stem cells, we characterise a recruitment hierarchy, where NSL-deposited histone acetylation enables BRD4 recruitment for transcription of constitutively active genes. Transcriptome analyses in Koolen-de Vries patient-derived fibroblasts reveals perturbations with a cellular homeostasis signature that are evoked by the NSL complex/BRD4 axis. We propose that BRD4 represents a conserved bridge between the NSL complex and transcription activation, and provide a new perspective in the understanding of their functions in healthy and diseased states.
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Affiliation(s)
- Aline Gaub
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France
| | - Cindy Colson
- Service Génétique, Génétique Clinique, CHU, Avenue Georges Clemenceau CS 30001, 14033, Caen, France.,Normandy University, UNICAEN, BIOTARGEN, Esplanade de la Paix CS 14032, 14032, Caen, France
| | - Matthew J Bird
- Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - James E Bradner
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Julien Thevenon
- CNRS UMR 5309, INSERM, U1209, Institute of Advanced Biosciences, Université Grenoble-Alpes CHU Grenoble, Allée des Alpes, 38700, La Tronche Grenoble, France
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
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Lalani SR. Other genomic disorders and congenital heart disease. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:107-115. [DOI: 10.1002/ajmg.c.31762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/09/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Seema R. Lalani
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
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Spirito G, Mangoni D, Sanges R, Gustincich S. Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data. BMC Bioinformatics 2019; 20:495. [PMID: 31757210 PMCID: PMC6873650 DOI: 10.1186/s12859-019-3113-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. RESULTS In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. CONCLUSION We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.
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Affiliation(s)
- Giovanni Spirito
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy.
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
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Pavlova GA, Popova JV, Andreyeva EN, Yarinich LA, Lebedev MO, Razuvaeva AV, Dubatolova TD, Oshchepkova AL, Pellacani C, Somma MP, Pindyurin AV, Gatti M. RNAi-mediated depletion of the NSL complex subunits leads to abnormal chromosome segregation and defective centrosome duplication in Drosophila mitosis. PLoS Genet 2019; 15:e1008371. [PMID: 31527906 PMCID: PMC6772098 DOI: 10.1371/journal.pgen.1008371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/01/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023] Open
Abstract
The Drosophila Nonspecific Lethal (NSL) complex is a major transcriptional regulator of housekeeping genes. It contains at least seven subunits that are conserved in the human KANSL complex: Nsl1/Wah (KANSL1), Dgt1/Nsl2 (KANSL2), Rcd1/Nsl3 (KANSL3), Rcd5 (MCRS1), MBD-R2 (PHF20), Wds (WDR5) and Mof (MOF/KAT8). Previous studies have shown that Dgt1, Rcd1 and Rcd5 are implicated in centrosome maintenance. Here, we analyzed the mitotic phenotypes caused by RNAi-mediated depletion of Rcd1, Rcd5, MBD-R2 or Wds in greater detail. Depletion of any of these proteins in Drosophila S2 cells led to defects in chromosome segregation. Consistent with these findings, Rcd1, Rcd5 and MBD-R2 RNAi cells showed reduced levels of both Cid/CENP-A and the kinetochore component Ndc80. In addition, RNAi against any of the four genes negatively affected centriole duplication. In Wds-depleted cells, the mitotic phenotypes were similar but milder than those observed in Rcd1-, Rcd5- or MBD-R2-deficient cells. RT-qPCR experiments and interrogation of published datasets revealed that transcription of many genes encoding centromere/kinetochore proteins (e.g., cid, Mis12 and Nnf1b), or involved in centriole duplication (e.g., Sas-6, Sas-4 and asl) is substantially reduced in Rcd1, Rcd5 and MBD-R2 RNAi cells, and to a lesser extent in wds RNAi cells. During mitosis, both Rcd1-GFP and Rcd5-GFP accumulate at the centrosomes and the telophase midbody, MBD-R2-GFP is enriched only at the chromosomes, while Wds-GFP accumulates at the centrosomes, the kinetochores, the midbody, and on a specific chromosome region. Collectively, our results suggest that the mitotic phenotypes caused by Rcd1, Rcd5, MBD-R2 or Wds depletion are primarily due to reduced transcription of genes involved in kinetochore assembly and centriole duplication. The differences in the subcellular localizations of the NSL components may reflect direct mitotic functions that are difficult to detect at the phenotypic level, because they are masked by the transcription-dependent deficiency of kinetochore and centriolar proteins. The Drosophila Nonspecific Lethal (NSL) complex is a conserved protein assembly that controls transcription of more than 4,000 housekeeping genes. We analyzed the mitotic functions of four genes, Rcd1, Rcd5, MBD-R2 and wds, encoding NSL subunits. Inactivation of these genes by RNA interference (RNAi) resulted in defects in both chromosome segregation and centrosome duplication. Our analyses indicate that RNAi against Rcd1, Rcd5 or MBD-R2 reduces transcription of genes involved in centromere/kinetochore assembly and centriole replication. During interphase, Rcd1, Rcd5, MBD-R2 and Wds are confined to the nucleus, as expected for transcription factors. However, during mitosis each of these proteins relocates to specific mitotic structures. Our results suggest that the four NSL components work together as a complex to stimulate transcription of genes encoding important mitotic determinants. However, the different localization of the proteins during mitosis suggests that they might have acquired secondary “moonlighting” functions that directly contribute to the mitotic process.
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Affiliation(s)
- Gera A. Pavlova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Julia V. Popova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
| | - Evgeniya N. Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Lyubov A. Yarinich
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Mikhail O. Lebedev
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Alyona V. Razuvaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana D. Dubatolova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
| | - Anastasiya L. Oshchepkova
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Novosibirsk, Russia
| | - Claudia Pellacani
- IBPM CNR c/o Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Maria Patrizia Somma
- IBPM CNR c/o Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Alexey V. Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail: (AVP); (MG)
| | - Maurizio Gatti
- IBPM CNR c/o Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- * E-mail: (AVP); (MG)
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Sadowski M, Kraft A, Szalaj P, Wlasnowolski M, Tang Z, Ruan Y, Plewczynski D. Spatial chromatin architecture alteration by structural variations in human genomes at the population scale. Genome Biol 2019; 20:148. [PMID: 31362752 PMCID: PMC6664780 DOI: 10.1186/s13059-019-1728-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/30/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The number of reported examples of chromatin architecture alterations involved in the regulation of gene transcription and in disease is increasing. However, no genome-wide testing has been performed to assess the abundance of these events and their importance relative to other factors affecting genome regulation. This is particularly interesting given that a vast majority of genetic variations identified in association studies are located outside coding sequences. This study attempts to address this lack by analyzing the impact on chromatin spatial organization of genetic variants identified in individuals from 26 human populations and in genome-wide association studies. RESULTS We assess the tendency of structural variants to accumulate in spatially interacting genomic segments and design an algorithm to model chromatin conformational changes caused by structural variations. We show that differential gene transcription is closely linked to the variation in chromatin interaction networks mediated by RNA polymerase II. We also demonstrate that CTCF-mediated interactions are well conserved across populations, but enriched with disease-associated SNPs. Moreover, we find boundaries of topological domains as relatively frequent targets of duplications, which suggest that these duplications can be an important evolutionary mechanism of genome spatial organization. CONCLUSIONS This study assesses the critical impact of genetic variants on the higher-order organization of chromatin folding and provides insight into the mechanisms regulating gene transcription at the population scale, of which local arrangement of chromatin loops seems to be the most significant. It provides the first insight into the variability of the human 3D genome at the population scale.
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Affiliation(s)
- Michal Sadowski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Agnieszka Kraft
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
| | - Przemyslaw Szalaj
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Centre for Innovative Research, Medical University of Bialystok, Kilinskiego 1, 15-089 Bialystok, Poland
- I-BioStat, Hasselt University, Agoralaan building D, BE3590 Diepenbeek, Belgium
| | - Michal Wlasnowolski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032 USA
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
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Sheikh BN, Akhtar A. The many lives of KATs - detectors, integrators and modulators of the cellular environment. Nat Rev Genet 2019; 20:7-23. [PMID: 30390049 DOI: 10.1038/s41576-018-0072-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Research over the past three decades has firmly established lysine acetyltransferases (KATs) as central players in regulating transcription. Recent advances in genomic sequencing, metabolomics, animal models and mass spectrometry technologies have uncovered unexpected new roles for KATs at the nexus between the environment and transcriptional regulation. Thousands of reversible acetylation sites have been mapped in the proteome that respond dynamically to the cellular milieu and maintain major processes such as metabolism, autophagy and stress response. Concurrently, researchers are continuously uncovering how deregulation of KAT activity drives disease, including cancer and developmental syndromes characterized by severe intellectual disability. These novel findings are reshaping our view of KATs away from mere modulators of chromatin to detectors of the cellular environment and integrators of diverse signalling pathways with the ability to modify cellular phenotype.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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Abstract
Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics. Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation. SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher-order chromatin organization such as topologically associating domains. As a result of these position effects, SVs can influence the expression of genes distant from the SV breakpoints, thereby causing disease. The impact of SVs on the 3D genome and on gene expression regulation has to be considered when interpreting the pathogenic potential of these variant types.
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Affiliation(s)
- Malte Spielmann
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.
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Sheikh BN, Guhathakurta S, Akhtar A. The non-specific lethal (NSL) complex at the crossroads of transcriptional control and cellular homeostasis. EMBO Rep 2019; 20:e47630. [PMID: 31267707 PMCID: PMC6607013 DOI: 10.15252/embr.201847630] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/10/2019] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
The functionality of chromatin is tightly regulated by post-translational modifications that modulate transcriptional output from target loci. Among the post-translational modifications of chromatin, reversible ε-lysine acetylation of histone proteins is prominent at transcriptionally active genes. Lysine acetylation is catalyzed by lysine acetyltransferases (KATs), which utilize the central cellular metabolite acetyl-CoA as their substrate. Among the KATs that mediate lysine acetylation, males absent on the first (MOF/KAT8) is particularly notable for its ability to acetylate histone 4 lysine 16 (H4K16ac), a modification that decompacts chromatin structure. MOF and its non-specific lethal (NSL) complex members have been shown to localize to gene promoters and enhancers in the nucleus, as well as to microtubules and mitochondria to regulate key cellular processes. Highlighting their importance, mutations or deregulation of NSL complex members has been reported in both human neurodevelopmental disorders and cancer. Based on insight gained from studies in human, mouse, and Drosophila model systems, this review discusses the role of NSL-mediated lysine acetylation in a myriad of cellular functions in both health and disease. Through these studies, the importance of the NSL complex in regulating core transcriptional and signaling networks required for normal development and cellular homeostasis is beginning to emerge.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
| | - Sukanya Guhathakurta
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
- Faculty of BiologyAlbert Ludwig University of FreiburgFreiburgGermany
| | - Asifa Akhtar
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
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Woodfin T, Stoops C, Philips JB, Lose E, Mikhail FM, Hurst A. Menkes disease complicated by concurrent Koolen-de Vries syndrome (17q21.31 deletion). Mol Genet Genomic Med 2019; 7:e829. [PMID: 31250568 PMCID: PMC6687649 DOI: 10.1002/mgg3.829] [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: 03/06/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 02/02/2023] Open
Abstract
Background Koolen‐de Vries (KdV) syndrome is caused by a 17q21.31 deletion leading to clinical symptoms of hypotonia and developmental delay and can present with abnormal hair texture. Menkes disease is an X‐linked recessive inherited disease caused by pathogenic variants in ATP7A, which leads to profound copper deficiency. Method We identified an infant male who presented with prematurity, hypotonia, and dysmorphic features for whom a family history of clinical Menkes disease was revealed after discussion with the clinical genetics team. Results Although initial first‐tier genetic testing identified Kdv syndrome (17q21.31 syndrome), the family history led the team to consider a second diagnostic possibility, and testing of ATP7A revealed a pathogenic variant (c.601C>T, p.R201X). Conclusion Menkes disease and KdV syndrome may both present with hypotonia and abnormal hair, in addition to seizures and failure to thrive. While these genetic conditions have overlapping clinical features, they have different natural histories and different therapeutic options. Here, we report on a patient affected with both disorders and review the diagnostic and therapeutic difficulties this presented.
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Affiliation(s)
- Taylor Woodfin
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Christine Stoops
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Joseph B Philips
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Edward Lose
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Anna Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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