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Miceli M, Failla P, Saccuzzo L, Galesi O, Amata S, Romano C, Bonaglia MC, Fichera M. Trait - driven analysis of the 2p15p16.1 microdeletion syndrome suggests a complex pattern of interactions between candidate genes. Genes Genomics 2023; 45:491-505. [PMID: 36807877 PMCID: PMC10027778 DOI: 10.1007/s13258-023-01369-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Individuals with the 2p15p16.1 microdeletion syndrome share a complex phenotype including neurodevelopmental delay, brain malformations, microcephaly, and autistic behavior. The analysis of the shortest region of overlap (SRO) between deletions in ~ 40 patients has led to the identification of two critical regions and four strongly candidate genes (BCL11A, REL, USP34 and XPO1). However, the delineation of their role in the occurrence of specific traits is hampered by their incomplete penetrance. OBJECTIVE To better delineate the role of hemizygosity of specific regions in selected traits by leveraging information both from penetrant and non - penetrant deletions. METHODS Deletions in patients that do not present a specific trait cannot contribute to delineate the SROs. We recently developed a probabilistic model that, by considering also the non - penetrant deletions, allows a more reliable assignment of peculiar traits to specific genomic segments. We apply this method adding two new patients to the published cases. RESULTS Our results delineate an intricate pattern of genotype - phenotype correlation where BCL11A emerges as the main gene for autistic behavior while USP34 and/or XPO1 haploinsufficiency are mainly associated with microcephaly, hearing loss and IUGR. BCL11A, USP34 and XPO1 genes are broadly related with brain malformations albeit with distinct patterns of brain damage. CONCLUSIONS The observed penetrance of deletions encompassing different SROs and that predicted when considering each single SRO as acting independently, may reflect a more complex model than the additive one. Our approach may improve the genotype/phenotype correlation and may help to identify specific pathogenic mechanisms in contiguous gene syndromes.
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Affiliation(s)
- Martina Miceli
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | | | - Lucia Saccuzzo
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | | | | | - Corrado Romano
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy.
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy.
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2
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Saia F, Prato A, Saccuzzo L, Madia F, Barone R, Fichera M, Rizzo R. Copy Number Variations in Children with Tourette Syndrome: Systematic Investigation in a Clinical Setting. Genes (Basel) 2023; 14:500. [PMID: 36833427 PMCID: PMC9956985 DOI: 10.3390/genes14020500] [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: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Tourette syndrome (TS) is a neurodevelopmental disturbance with heterogeneous and not completely known etiology. Clinical and molecular appraisal of affected patients is mandatory for outcome amelioration. The current study aimed to understand the molecular bases underpinning TS in a vast cohort of pediatric patients with TS. Molecular analyses included array-CGH analyses. The primary goal was to define the neurobehavioral phenotype of patients with or without pathogenic copy number variations (CNVs). Moreover, we compared the CNVs with CNVs described in the literature in neuropsychiatric disorders, including TS, to describe an effective clinical and molecular characterization of patients for prognostic purposes and for correctly taking charge. Moreover, this study showed that rare deletions and duplications focusing attention on significant genes for neurodevelopment had a statistically higher occurrence in children with tics and additional comorbidities. In our cohort, we determined an incidence of potentially causative CNVs of about 12%, in line with other literature studies. Clearly, further studies are needed to delineate the genetic background of patients with tic disorders in a superior way to elucidate the complex genetic architecture of these disorders, to describe the outcome, and to identify new possible therapeutic targets.
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Affiliation(s)
- Federica Saia
- Child and Adolescent Neurology and Psychiatric Section, Department of Clinical and Experimental Medicine, Catania University, 95124 Catania, Italy
| | - Adriana Prato
- Child and Adolescent Neurology and Psychiatric Section, Department of Clinical and Experimental Medicine, Catania University, 95124 Catania, Italy
- Department of Cognitive Sciences, Psychology, Education and Cultural Studies, University of Messina, 98121 Messina, Italy
| | - Lucia Saccuzzo
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 95124 Catania, Italy
| | - Francesca Madia
- Laboratory of Neurogenetics and Neuroscience, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Rita Barone
- Child and Adolescent Neurology and Psychiatric Section, Department of Clinical and Experimental Medicine, Catania University, 95124 Catania, Italy
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 95124 Catania, Italy
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Renata Rizzo
- Child and Adolescent Neurology and Psychiatric Section, Department of Clinical and Experimental Medicine, Catania University, 95124 Catania, Italy
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3
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Bruce L, Peter B. Three children with different de novo BCL11A variants and diverse developmental phenotypes, but shared global motor discoordination and apraxic speech: Evidence for a functional gene network influencing the developing cerebellum and motor and auditory cortices. Am J Med Genet A 2022; 188:3401-3415. [PMID: 35856171 DOI: 10.1002/ajmg.a.62904] [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: 09/15/2021] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 01/31/2023]
Abstract
BCL11A is implicated in BCL11A-Related Intellectual Development Disorder (BCL11A-IDD). Previously reported cases had various types of BCL11A variants (copy-number variations [CNVs], singlenucleotide variants [SNVs]). Phenotypes included global, cognitive, and motor delays, autism spectrum disorder (ASD), craniofacial dysmorphology, and speech and language delays described generally, with only two reports specifying childhood apraxia of speech (CAS). Here, we present three additional children with CAS and de novo BCL11A variants, a p.Ala182Thr nonconservative missense and a p.GLu611.Ter nonsense variant, both in exon 4, and a 106 kb deletion harboring exons 1 and 2. All three children have fine and gross motor discoordination, feeding difficulties, and visual motor disorders. Intellectual and learning disabilities and disordered language skills were seen only in the child with the missense variant and the child with the deletion. These findings align with, and expand, previous findings in that BCL11A variants have significant and highly penetrant apraxic effects across motor systems, consistent with cerebellar involvement. The deletion of exons 1 and 2 is the smallest BCL11A CNV with the full phenotypic expression reported to date. The present results support previous findings in that BCL11A-IDD can result from BCL11A variants regardless of type (deletion, SNVs). A gene expression study shows that BCL11 is expressed highly in the early developing cerebellum and primary motor and auditory cortices. Significant co-expression rates in these regions with genes previously implicated in disorders of spoken language and in ASD support the phenotypic overlaps in children with BCL11A-IDD, CAS, and ASD.
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Affiliation(s)
- Laurel Bruce
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Beate Peter
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
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4
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Ye Y, Lui VCH, Tam PKH. Pathogenesis of Choledochal Cyst: Insights from Genomics and Transcriptomics. Genes (Basel) 2022; 13:genes13061030. [PMID: 35741793 PMCID: PMC9223186 DOI: 10.3390/genes13061030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/10/2022] Open
Abstract
Choledochal cysts (CC) is characterized by extra- and/or intra-hepatic b\ile duct dilations. There are two main theories, “pancreaticobiliary maljunction” and “congenital stenosis of bile ducts” proposed for the pathogenesis of CC. Although family cases or CC associated with other anomalies have been reported, the molecular pathogenesis of CC is still poorly understood. Recent advances in transcriptomics and genomics analysis platforms have unveiled key expression signatures/genes/signaling pathways in the pathogenesis of human diseases including CC. This review summarizes insights from genomics and transcriptomics studies into the pathogenesis of CC, with the aim to improve (i) our understanding of its underlying complex pathomechanisms, and (ii) clinical management of different subtypes of CC, in particular their associated hepatic fibrotic change and their risk of malignancy transformation.
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Affiliation(s)
- Yongqin Ye
- Faculty of Medicine, Macau University of Science and Technology, Macau, China;
- Department of Surgery, School of Clinical Medicine, University of Hong Kong, Hong Kong, China;
| | - Vincent Chi Hang Lui
- Department of Surgery, School of Clinical Medicine, University of Hong Kong, Hong Kong, China;
| | - Paul Kwong Hang Tam
- Faculty of Medicine, Macau University of Science and Technology, Macau, China;
- Correspondence:
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5
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Niarchou M, Gustavson DE, Sathirapongsasuti JF, Anglada-Tort M, Eising E, Bell E, McArthur E, Straub P, McAuley JD, Capra JA, Ullén F, Creanza N, Mosing MA, Hinds DA, Davis LK, Jacoby N, Gordon RL. Genome-wide association study of musical beat synchronization demonstrates high polygenicity. Nat Hum Behav 2022; 6:1292-1309. [PMID: 35710621 PMCID: PMC9489530 DOI: 10.1038/s41562-022-01359-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/21/2022] [Indexed: 02/02/2023]
Abstract
Moving in synchrony to the beat is a fundamental component of musicality. Here we conducted a genome-wide association study to identify common genetic variants associated with beat synchronization in 606,825 individuals. Beat synchronization exhibited a highly polygenic architecture, with 69 loci reaching genome-wide significance (P < 5 × 10-8) and single-nucleotide-polymorphism-based heritability (on the liability scale) of 13%-16%. Heritability was enriched for genes expressed in brain tissues and for fetal and adult brain-specific gene regulatory elements, underscoring the role of central-nervous-system-expressed genes linked to the genetic basis of the trait. We performed validations of the self-report phenotype (through separate experiments) and of the genome-wide association study (polygenic scores for beat synchronization were associated with patients algorithmically classified as musicians in medical records of a separate biobank). Genetic correlations with breathing function, motor function, processing speed and chronotype suggest shared genetic architecture with beat synchronization and provide avenues for new phenotypic and genetic explorations.
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Affiliation(s)
- Maria Niarchou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA. .,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Daniel E. Gustavson
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | | | - Manuel Anglada-Tort
- grid.461782.e0000 0004 1795 8610Computational Auditory Perception Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Else Eising
- grid.419550.c0000 0004 0501 3839Department of Language and Genetics, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Eamonn Bell
- grid.21729.3f0000000419368729Department of Music, Columbia University, New York, NY USA ,grid.8250.f0000 0000 8700 0572Department of Computer Science, Durham University, Durham, UK
| | - Evonne McArthur
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Peter Straub
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | | | - J. Devin McAuley
- grid.17088.360000 0001 2150 1785Department of Psychology, Michigan State University, East Lansing, MI USA
| | - John A. Capra
- grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Epidemiology & Biostatistics, University of California, San Francisco, CA USA
| | - Fredrik Ullén
- grid.465198.7Department of Neuroscience, Karolinska Institutet, Solna, Sweden ,grid.461782.e0000 0004 1795 8610Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Nicole Creanza
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN USA
| | - Miriam A. Mosing
- grid.465198.7Department of Neuroscience, Karolinska Institutet, Solna, Sweden ,grid.461782.e0000 0004 1795 8610Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany ,grid.1008.90000 0001 2179 088XMelbourne School of Psychological Sciences, University of Melbourne, Melbourne, Victoria Australia
| | - David A. Hinds
- grid.420283.f0000 0004 0626 085823andMe, Inc, Sunnyvale, CA USA
| | - Lea K. Davis
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN USA
| | - Nori Jacoby
- grid.461782.e0000 0004 1795 8610Computational Auditory Perception Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Reyna L. Gordon
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Otolaryngology—Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Psychology, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN USA
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6
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Yamazawa K, Shimizu K, Ohashi H, Haruna H, Inoue S, Murakami H, Matsunaga T, Iwata T, Tsunoda K, Fujinami K. A Japanese boy with double diagnoses of 2p15p16.1 microdeletion syndrome and RP2-associated retinal disorder. Hum Genome Var 2021; 8:46. [PMID: 34921139 PMCID: PMC8683409 DOI: 10.1038/s41439-021-00178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/16/2021] [Accepted: 11/21/2021] [Indexed: 11/24/2022] Open
Abstract
2p15p16.1 microdeletion syndrome is a recently recognized congenital disorder characterized by developmental delay and dysmorphic features. RP2-associated retinal disorder (RP2-RD) is an X-linked inherited retinal disease with a childhood onset caused by a loss-of-function variant in the RP2 gene. Here, we describe a 14-year-old boy with double diagnoses of 2p15p16.1 microdeletion syndrome and RP2-RD. The recurrence risk of each condition and the indication for potential therapeutic options for RP2-RD are discussed.
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Affiliation(s)
- Kazuki Yamazawa
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan. .,Department of Pediatrics, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.
| | - Kenji Shimizu
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan.,Division of Medical Genetics and Cytogenetics, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | - Hidenori Haruna
- Department of Pediatrics and Adolescent Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Satomi Inoue
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Haruka Murakami
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Tatsuo Matsunaga
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kaoru Fujinami
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan. .,Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan. .,UCL Institute of Ophthalmology, University College London, London, United Kingdom.
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7
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Abstract
Studies of the major hemoglobin disorders, β-thalassemia and sickle cell disease (SCD), have laid a foundation for molecular medicine. While enormous progress has been made in understanding gene structure and regulation, translating molecular insights to therapy for the many individuals affected with these disorders has been challenging. Advances in three activities have recently converged to bring novel genetic and potentially curative treatments to clinical trials. First, improved lentiviral vectors for gene transfer into hematopoietic stem cells have revived somatic gene therapy for blood disorders. Second, elucidation of regulatory factors and mechanisms that control the normal developmental switch from fetal to adult hemoglobin has provided a route to reactivation of the fetal form for therapy. Third, revolutionary methods of gene engineering permit molecular insights to be leveraged for patients. Here I review how the promise of molecular medicine to bring transformative treatments to the clinical arena is finally being realized.
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Affiliation(s)
- Stuart H Orkin
- Dana Farber/Boston Children's Cancer & Blood Disorders Center, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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8
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Widespread transcriptional disruption of the microRNA biogenesis machinery in brain and peripheral tissues of individuals with schizophrenia. Transl Psychiatry 2020; 10:376. [PMID: 33149139 PMCID: PMC7642431 DOI: 10.1038/s41398-020-01052-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/16/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
In schizophrenia, altered transcription in brain and peripheral tissues may be due to altered expression of the microRNA biogenesis machinery genes. In this study, we explore the expression of these genes both at the cerebral and peripheral levels. We used shinyGEO application to analyze gene expression from ten Gene Expression Omnibus datasets, in order to perform differential expression analyses for eight genes encoding the microRNA biogenesis machinery. First, we compared expression of the candidate genes between control subjects and individuals with schizophrenia in postmortem cerebral samples from seven different brain regions. Then, we compared the expression of the candidate genes between control subjects and individuals with schizophrenia in three peripheral tissues. In brain and peripheral tissues of individuals with schizophrenia, we report distinct altered expression patterns of the microRNA biogenesis machinery genes. In the dorsolateral prefrontal cortex, associative striatum and cerebellum of individuals with schizophrenia, we observed an overexpression pattern of some candidate genes suggesting a heightened miRNA production in these brain regions. Additionally, mixed transcriptional abnormalities were identified in the hippocampus. Moreover, in the blood and olfactory epithelium of individuals with schizophrenia, we observed distinct aberrant transcription patterns of the candidate genes. Remarkably, in individuals with schizophrenia, we report DICER1 overexpression in the dorsolateral prefrontal cortex, hippocampus and cerebellum as well as a congruent DICER1 upregulation in the blood compartment suggesting that it may represent a peripheral marker. Transcriptional disruption of the miRNA biogenesis machinery may contribute to schizophrenia pathogenesis both in brain and peripheral tissues.
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9
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Li Q, Wang M, Xue H, Liu W, Guo Y, Xu R, Shao B, Yuan Q. Ubiquitin-Specific Protease 34 Inhibits Osteoclast Differentiation by Regulating NF-κB Signaling. J Bone Miner Res 2020; 35:1597-1608. [PMID: 32212276 DOI: 10.1002/jbmr.4015] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 02/05/2023]
Abstract
The ubiquitination and deubiquitination enzymes ensure the stability and proper function of most cellular proteins. Disturbance of either enzyme compromises tissue homeostasis. We recently have identified that the ubiquitin-specific protease 34 (USP34) contributes to bone formation by promoting osteogenic differentiation of mesenchymal stem cells. However, its role in bone resorption, which couples bone formation, remains unknown. Here we show that knockdown of Usp34 promotes osteoclast differentiation of RAW264.7 cells. Conditional knockout of Usp34 in bone marrow-derived macrophages (BMMs) or in osteoclasts leads to elevated osteoclast function and low bone mass. Mechanically, we identify that USP34 restrains NF-κB signaling by deubiquitinating and stabilizing the NF-κB inhibitor alpha (IκBα). Overexpression of IκBα represses osteoclastic hyperfunction of Usp34-deficient RAW264.7 cells. Collectively, our results show that USP34 inhibits osteoclastogenesis by regulating NF-κB signaling. © 2020 American Society for Bone and Mineral Research.
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Affiliation(s)
- Qiwen Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mengyuan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Stomatology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Hanxiao Xue
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Weiqing Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuchen Guo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ruoshi Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bin Shao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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10
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Courchesne E, Pramparo T, Gazestani VH, Lombardo MV, Pierce K, Lewis NE. The ASD Living Biology: from cell proliferation to clinical phenotype. Mol Psychiatry 2019; 24:88-107. [PMID: 29934544 PMCID: PMC6309606 DOI: 10.1038/s41380-018-0056-y] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 02/08/2018] [Accepted: 02/19/2018] [Indexed: 12/17/2022]
Abstract
Autism spectrum disorder (ASD) has captured the attention of scientists, clinicians and the lay public because of its uncertain origins and striking and unexplained clinical heterogeneity. Here we review genetic, genomic, cellular, postmortem, animal model, and cell model evidence that shows ASD begins in the womb. This evidence leads to a new theory that ASD is a multistage, progressive disorder of brain development, spanning nearly all of prenatal life. ASD can begin as early as the 1st and 2nd trimester with disruption of cell proliferation and differentiation. It continues with disruption of neural migration, laminar disorganization, altered neuron maturation and neurite outgrowth, disruption of synaptogenesis and reduced neural network functioning. Among the most commonly reported high-confidence ASD (hcASD) genes, 94% express during prenatal life and affect these fetal processes in neocortex, amygdala, hippocampus, striatum and cerebellum. A majority of hcASD genes are pleiotropic, and affect proliferation/differentiation and/or synapse development. Proliferation and subsequent fetal stages can also be disrupted by maternal immune activation in the 1st trimester. Commonly implicated pathways, PI3K/AKT and RAS/ERK, are also pleiotropic and affect multiple fetal processes from proliferation through synapse and neural functional development. In different ASD individuals, variation in how and when these pleiotropic pathways are dysregulated, will lead to different, even opposing effects, producing prenatal as well as later neural and clinical heterogeneity. Thus, the pathogenesis of ASD is not set at one point in time and does not reside in one process, but rather is a cascade of prenatal pathogenic processes in the vast majority of ASD toddlers. Despite this new knowledge and theory that ASD biology begins in the womb, current research methods have not provided individualized information: What are the fetal processes and early-age molecular and cellular differences that underlie ASD in each individual child? Without such individualized knowledge, rapid advances in biological-based diagnostic, prognostic, and precision medicine treatments cannot occur. Missing, therefore, is what we call ASD Living Biology. This is a conceptual and paradigm shift towards a focus on the abnormal prenatal processes underlying ASD within each living individual. The concept emphasizes the specific need for foundational knowledge of a living child's development from abnormal prenatal beginnings to early clinical stages. The ASD Living Biology paradigm seeks this knowledge by linking genetic and in vitro prenatal molecular, cellular and neural measurements with in vivo post-natal molecular, neural and clinical presentation and progression in each ASD child. We review the first such study, which confirms the multistage fetal nature of ASD and provides the first in vitro fetal-stage explanation for in vivo early brain overgrowth. Within-child ASD Living Biology is a novel research concept we coin here that advocates the integration of in vitro prenatal and in vivo early post-natal information to generate individualized and group-level explanations, clinically useful prognoses, and precision medicine approaches that are truly beneficial for the individual infant and toddler with ASD.
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Affiliation(s)
- Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California, San Diego, 8110 La Jolla Shores Drive, Suite 201, La Jolla, CA, 92037, USA.
| | - Tiziano Pramparo
- Autism Center of Excellence, Department of Neuroscience, University of California, San Diego, 8110 La Jolla Shores Drive, Suite 201, La Jolla, CA, 92037, USA
| | - Vahid H Gazestani
- Autism Center of Excellence, Department of Neuroscience, University of California, San Diego, 8110 La Jolla Shores Drive, Suite 201, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Michael V Lombardo
- Department of Psychology, Center for Applied Neuroscience, University of Cyprus, Nicosia, Cyprus
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California, San Diego, 8110 La Jolla Shores Drive, Suite 201, La Jolla, CA, 92037, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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11
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Chromosome 2p15-p16.1 microduplication in a boy with congenital anomalies: Is it a distinctive syndrome? Eur J Med Genet 2019; 62:47-54. [PMID: 29864511 DOI: 10.1016/j.ejmg.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/17/2022]
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12
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Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet 2018; 51:106-116. [PMID: 30559488 PMCID: PMC6309590 DOI: 10.1038/s41588-018-0288-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/23/2018] [Indexed: 12/11/2022]
Abstract
We combined de novo mutation (DNM) data from 10,927 individuals with developmental delay and autism to identify 253 candidate neurodevelopmental disease genes with an excess of missense and/or likely gene-disruptive (LGD) mutations. Of these genes, 124 reach exome-wide significance (P < 5 × 10-7) for DNM. Intersecting these results with copy number variation (CNV) morbidity data shows an enrichment for genomic disorder regions (30/253, likelihood ratio (LR) +1.85, P = 0.0017). We identify genes with an excess of missense DNMs overlapping deletion syndromes (for example, KIF1A and the 2q37 deletion) as well as duplication syndromes, such as recurrent MAPK3 missense mutations within the chromosome 16p11.2 duplication, recurrent CHD4 missense DNMs in the 12p13 duplication region, and recurrent WDFY4 missense DNMs in the 10q11.23 duplication region. Network analyses of genes showing an excess of DNMs highlights functional networks, including cell-specific enrichments in the D1+ and D2+ spiny neurons of the striatum.
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Morgan AT, Webster R. Aetiology of childhood apraxia of speech: A clinical practice update for paediatricians. J Paediatr Child Health 2018; 54:1090-1095. [PMID: 30294994 DOI: 10.1111/jpc.14150] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 02/03/2023]
Abstract
Childhood apraxia of speech (CAS) is a rare disorder of childhood that can leave a watermark of the impacts throughout the lifetime. Since being first described in the 1950s, aetiological insights have been limited. At a neurobiological level, clinical MRI scans fail to reveal overt neural anomalies in individual cases with CAS, although quantitative MRI methods have revealed subtle brain anomalies at a group level. Dramatic insights, however, occurred in the past decade from the discovery of genetic pathways underlying the phenotype. Several single genes and copy number-variant conditions are now associated with CAS either in relative isolation, as in the case of FOXP2 variants, or most typically in association with other neurodevelopmental conditions, such as epilepsy, intellectual disability, motor impairment and autism. CAS requires careful differential diagnosis from other childhood speech disorders, but when a severe and persistent diagnosis is confirmed, a genetic aetiology should increasingly be pursued.
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Affiliation(s)
- Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Audiology and Speech Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Webster
- Department of Neurology and Neurosurgery, Children's Hospital, Sydney, New South Wales, Australia
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