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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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Wang J, Jia C, Gao Q, Zhang J, Gu X. iASPP regulates neurite development by interacting with Spectrin proteins. Front Mol Neurosci 2023; 16:1154770. [PMID: 37284462 PMCID: PMC10240065 DOI: 10.3389/fnmol.2023.1154770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/24/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction Since its discovery in 1999, a substantial body of research has shown that iASPP is highly expressed in various kinds of tumors, interacts with p53, and promotes cancer cell survival by antagonizing the apoptotic activity of p53. However, its role in neurodevelopment is still unknown. Methods We studied the role of iASPP in neuronal differentiation through different neuronal differentiation cellular models, combined with immunohistochemistry, RNA interference and gene overexpression, and studied the molecular mechanism involved in the regulation of neuronal development by iASPP through coimmunoprecipitation coupled with mass spectrometry (CoIP-MS) and coimmunoprecipitation (CoIP). Results In this study, we found that the expression of iASPP gradually decreased during neuronal development. iASPP silencing promotes neuronal differentiation, while its overexpression inhibited neurite differentiation in a variety of neuronal differentiation cellular models. iASPP associated with the cytoskeleton-related protein Sptan1 and dephosphorylated the serine residues in the last spectrin repeat domain of Sptan1 by recruiting PP1. The non-phosphorylated and phosphomimetic mutant form of Sptbn1 inhibited and promoted neuronal cell development respectively. Conclusion Overall, we demonstrate that iASPP suppressed neurite development by inhibiting phosphorylation of Sptbn1.
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Affiliation(s)
- Junhao Wang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Chunhong Jia
- Department of Neonatology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiong Gao
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jiwen Zhang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xi Gu
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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Expanding the Clinical Phenotype of 19q Interstitial Deletions: A New Case with 19q13.32-q13.33 Deletion and Short Review of the Literature. Genes (Basel) 2022; 13:genes13020212. [PMID: 35205257 PMCID: PMC8872157 DOI: 10.3390/genes13020212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/19/2022] Open
Abstract
19q13 microdeletion syndrome is a very rare genetic disease characterized by pre- and postnatal growth retardation, intellectual disability, expressive language impairment, ectodermal dysplasia, and slender habitus. Since the description of the first case in 1998, less than 30 cases have been reported worldwide. This article aims to review the knowledge gathered so far on this subject and to present the case of a 10-year-old girl admitted to the National University Center for Children Neurorehabilitation “Dr. Nicolae Robanescu” in November of 2018 who presented a slender habitus, growth retardation, facial dysmorphism, skeletal abnormalities, and ectodermal dysplasia. Array-CGH analysis revealed a 1.53 Mb deletion in the 19q13.32-q13.33 region. MLPA for the FKRP gene revealed that the microdeletion was de novo. The patient’s phenotype overlapped with the clinical features of 19q13 microdeletion syndrome. To our knowledge, this is the first case of 19q13 microdeletion syndrome to ever be reported in Romania. We believe our case presents additional features that have never been previously reported in this syndrome, namely, dilatation of the third ventricle and subependymal cyst, left iris coloboma, and tracheomalacia. Moreover, unlike the other 19q13 microdeletion cases that presented with dystonia, our patient also presented dystonia but, interestingly, without having haploinsufficiency of the KMT2B gene.
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Lawrence AJ. Letter to the editor: Comments on - Regulation of habenular G-protein gamma 8 on learning and memory via modulation of the central acetylcholine system. Mol Psychiatry 2022; 27:1871-1872. [PMID: 35115702 PMCID: PMC9126801 DOI: 10.1038/s41380-022-01451-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/04/2022] [Accepted: 01/14/2022] [Indexed: 11/13/2022]
Affiliation(s)
- Andrew J. Lawrence
- grid.418025.a0000 0004 0606 5526Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XFlorey Department of Neuroscience & Mental Health, University of Melbourne, Parkville, VIC 3052 Australia
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Dai L, Zhang D, Wu Z, Guan X, Ma M, Li L, Zhang Y, Bai Y, Guo H. A Tiered Genetic Screening Strategy for the Molecular Diagnosis of Intellectual Disability in Chinese Patients. Front Genet 2021; 12:669217. [PMID: 34630504 PMCID: PMC8495063 DOI: 10.3389/fgene.2021.669217] [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: 02/18/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023] Open
Abstract
Objective: Intellectual disability (ID) is one of the most common developmental disabilities. To identify the genetic etiology of IDs in Chongqing, we conducted a multistage study in Chinese Han patients. Methods: We collected the clinical and etiological data of 1665 ID patients, including 1,604 from the disabled children evaluation center and 61 from the pediatric rehabilitation unit. Routine genetic screening results were obtained, including karyotype and candidate gene analysis. Then 105 idiopathic cases with syndromic and severe ID/developmental delay (DD) were selected and tested by chromosomal microarray (CMA) and whole exome sequencing (WES) sequentially. The pathogenicity of the CNVs and SNVs were evaluated according to ACMG guidelines. Results: Molecular diagnosis was made by routine genetic screening in 216 patients, including 196 chromosomal syndromes. Among the 105 idiopathic patients, 49 patients with pathogenic/likely pathogenic CNVs and 21 patients with VUS were identified by CMA. Twenty-six pathogenic CNVs underlying well-known syndromic cases, such as Williams-Beuren syndrome, were confirmed by multiplex ligation-dependent probe amplification (MLPA). Nine novel mutations were identified by WES in thirty-fix CNV-negative ID cases. Conclusions: The study illustrated the genetic aberrations distribution of a large ID cohort in Chongqing. Compared with conventional or single methods, a tiered high-throughput diagnostic strategy was developed to greatly improve the diagnostic yields and extend the variation spectrum for idiopathic syndromic ID cases.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Danyan Zhang
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China.,Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Zhifeng Wu
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xingying Guan
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Mingfu Ma
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Lianbing Li
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Yuping Zhang
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
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Regulation of habenular G-protein gamma 8 on learning and memory via modulation of the central acetylcholine system. Mol Psychiatry 2021; 26:3737-3750. [PMID: 32989244 DOI: 10.1038/s41380-020-00893-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/24/2020] [Accepted: 09/15/2020] [Indexed: 01/19/2023]
Abstract
Guanine nucleotide binding protein (G protein) gamma 8 (Gng8) is a subunit of G proteins and expressed in the medial habenula (MHb) and interpeduncular nucleus (IPN). Recent studies have demonstrated that Gng8 is involved in brain development; however, the roles of Gng8 on cognitive function have not yet been addressed. In the present study, we investigated the expression of Gng8 in the brain and found that Gng8 was predominantly expressed in the MHb-IPN circuit of the mouse brain. We generated Gng8 knockout (KO) mice by CRISPR/Cas9 system in order to assess the role of Gng8 on cognitive function. Gng8 KO mice exhibited deficiency in learning and memory in passive avoidance and Morris water maze tests. In addition, Gng8 KO mice significantly reduced long-term potentiation (LTP) in the hippocampus compared to that of wild-type (WT) mice. Furthermore, we observed that levels of acetylcholine (ACh) and choline acetyltransferase (ChAT) in the MHb and IPN of Gng8 KO mice were significantly decreased, compared to WT mice. The administration of nAChR α4β2 agonist A85380 rescued memory impairment in the Gng8 KO mice, suggesting that Gng8 regulates cognitive function via modulation of cholinergic activity. Taken together, Gng8 is a potential therapeutic target for memory-related diseases and/or neurodevelopmental diseases.
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Tennakoon M, Senarath K, Kankanamge D, Ratnayake K, Wijayaratna D, Olupothage K, Ubeysinghe S, Martins-Cannavino K, Hébert TE, Karunarathne A. Subtype-dependent regulation of Gβγ signalling. Cell Signal 2021; 82:109947. [PMID: 33582184 PMCID: PMC8026654 DOI: 10.1016/j.cellsig.2021.109947] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 01/04/2023]
Abstract
G protein-coupled receptors (GPCRs) transmit information to the cell interior by transducing external signals to heterotrimeric G protein subunits, Gα and Gβγ subunits, localized on the inner leaflet of the plasma membrane. Though the initial focus was mainly on Gα-mediated events, Gβγ subunits were later identified as major contributors to GPCR-G protein signalling. A broad functional array of Gβγ signalling has recently been attributed to Gβ and Gγ subtype diversity, comprising 5 Gβ and 12 Gγ subtypes, respectively. In addition to displaying selectivity towards each other to form the Gβγ dimer, numerous studies have identified preferences of distinct Gβγ combinations for specific GPCRs, Gα subtypes and effector molecules. Importantly, Gβ and Gγ subtype-dependent regulation of downstream effectors, representing a diverse range of signalling pathways and physiological functions have been found. Here, we review the literature on the repercussions of Gβ and Gγ subtype diversity on direct and indirect regulation of GPCR/G protein signalling events and their physiological outcomes. Our discussion additionally provides perspective in understanding the intricacies underlying molecular regulation of subtype-specific roles of Gβγ signalling and associated diseases.
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Affiliation(s)
- Mithila Tennakoon
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Kanishka Senarath
- Genetics and Molecular Biology Unit, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Dinesh Kankanamge
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Kasun Ratnayake
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dhanushan Wijayaratna
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Koshala Olupothage
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | - Sithurandi Ubeysinghe
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA
| | | | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.
| | - Ajith Karunarathne
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606, USA.
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Molinaro P, Natale S, Serani A, Calabrese L, Secondo A, Tedeschi V, Valsecchi V, Pannaccione A, Scorziello A, Annunziato L. Genetically modified mice to unravel physiological and pathophysiological roles played by NCX isoforms. Cell Calcium 2020; 87:102189. [PMID: 32199207 DOI: 10.1016/j.ceca.2020.102189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 03/01/2020] [Indexed: 11/30/2022]
Abstract
Since the discovery of the three isoforms of the Na+/Ca2+ exchanger, NCX1, NCX2 and NCX3 in 1990s, many studies have been devoted to identifying their specific roles in different tissues under several physiological or pathophysiological conditions. In particular, several seminal experimental works laid the foundation for better understanding gene and protein structures, tissue distribution, and regulatory functions of each antiporter isoform. On the other hand, despite the efforts in the development of specific compounds selectively targeting NCX1, NCX2 or NCX3 to test their physiological or pathophysiological roles, several drawbacks hampered the achievement of these goals. In fact, at present no isoform-specific compounds have been yet identified. Moreover, these compounds, despite their potency, possess some nonspecific actions against other ion antiporters, ion channels, and channel receptors. As a result, it is difficult to discriminate direct effects of inhibition/activation of NCX isoforms from the inhibitory or stimulatory effects exerted on other antiporters, channels, receptors, or enzymes. To overcome these difficulties, some research groups used transgenic, knock-out and knock-in mice for NCX isoforms as the most straightforward and fruitful strategy to characterize the biological role exerted by each antiporter isoform. The present review will survey the techniques used to study the roles of NCXs and the current knowledge obtained from these genetic modified mice focusing on the advantages obtained with these strategies in understanding the contribution exerted by each isoform.
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Affiliation(s)
- Pasquale Molinaro
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy.
| | - Silvia Natale
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
| | - Angelo Serani
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
| | - Lucrezia Calabrese
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
| | - Agnese Secondo
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
| | - Valentina Tedeschi
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
| | - Valeria Valsecchi
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
| | - Anna Pannaccione
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
| | - Antonella Scorziello
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, 80131, Naples, Italy
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Al-Naama N, Mackeh R, Kino T. C 2H 2-Type Zinc Finger Proteins in Brain Development, Neurodevelopmental, and Other Neuropsychiatric Disorders: Systematic Literature-Based Analysis. Front Neurol 2020; 11:32. [PMID: 32117005 PMCID: PMC7034409 DOI: 10.3389/fneur.2020.00032] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are multifaceted pathologic conditions manifested with intellectual disability, autistic features, psychiatric problems, motor dysfunction, and/or genetic/chromosomal abnormalities. They are associated with skewed neurogenesis and brain development, in part through dysfunction of the neural stem cells (NSCs) where abnormal transcriptional regulation on key genes play significant roles. Recent accumulated evidence highlights C2H2-type zinc finger proteins (C2H2-ZNFs), the largest transcription factor family in humans, as important targets for the pathologic processes associated with NDDs. In this review, we identified their significant accumulation (74 C2H2-ZNFs: ~10% of all human member proteins) in brain physiology and pathology. Specifically, we discuss their physiologic contribution to brain development, particularly focusing on their actions in NSCs. We then explain their pathologic implications in various forms of NDDs, such as morphological brain abnormalities, intellectual disabilities, and psychiatric disorders. We found an important tendency that poly-ZNFs and KRAB-ZNFs tend to be involved in the diseases that compromise gross brain structure and human-specific higher-order functions, respectively. This may be consistent with their characteristic appearance in the course of species evolution and corresponding contribution to these brain activities.
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Affiliation(s)
- Njoud Al-Naama
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Rafah Mackeh
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Tomoshige Kino
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
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Baizabal-Carvallo JF, Alonso-Juarez M. Generalized dystonia associated with mutation in the histone methyltransferase gene KMT2B (DYT28) and white matter abnormalities. Parkinsonism Relat Disord 2018; 49:116-117. [PMID: 29396090 DOI: 10.1016/j.parkreldis.2018.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 12/14/2022]
Affiliation(s)
- José Fidel Baizabal-Carvallo
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, USA; University of Guanajuato, Mexico.
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Armes JE, Williams M, Price G, Wallis T, Gallagher R, Matsika A, Joy C, Galea M, Gardener G, Leach R, Swagemakers SM, Tearle R, Stubbs A, Harraway J, van der Spek PJ, Venter DJ. Application of Whole Genome Sequencing Technology in the Investigation of Genetic Causes of Fetal, Perinatal, and Early Infant Death. Pediatr Dev Pathol 2018. [PMID: 28641477 DOI: 10.1177/1093526617715528] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Death in the fetal, perinatal, and early infant age-group has a multitude of causes, a proportion of which is presumed to be genetic. Defining a specific genetic aberration leading to the death is problematic at this young age, due to limited phenotype-genotype correlation inherent in the underdeveloped phenotype, the inability to assess certain phenotypic traits after death, and the problems of dealing with rare disorders. In this study, our aim was to increase the yield of identification of a defined genetic cause of an early death. Therefore, we employed whole genome sequencing and bioinformatic filtering techniques as a comprehensive, unbiased genetic investigation into 16 fetal, perinatal, and early infant deaths, which had undergone a full autopsy. A likely genetic cause was identified in two cases (in genes; COL2A1 and RYR1) and a speculative genetic cause in a further six cases (in genes: ARHGAP35, BBS7, CASZ1, CRIM1, DHCR7, HADHB, HAPLN3, HSPG2, MYO18B, and SRGAP2). This investigation indicates that whole genome sequencing is a significantly enabling technology when determining genetic causes of early death.
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Affiliation(s)
- Jane E Armes
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia.,2 Mater Research Institute, University of Queensland, Queensland, Australia.,3 School of Medicine, University of Queensland, Queensland, Australia
| | - Mark Williams
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia.,2 Mater Research Institute, University of Queensland, Queensland, Australia
| | - Gareth Price
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia
| | - Tristan Wallis
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia
| | - Renee Gallagher
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia
| | - Admire Matsika
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia
| | - Christopher Joy
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia
| | - Melanie Galea
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia
| | - Glenn Gardener
- 2 Mater Research Institute, University of Queensland, Queensland, Australia.,4 Centre for Maternal Fetal Medicine, Mater Health, South Brisbane, Queensland, Australia
| | - Rick Leach
- 5 Complete Genomics Inc, Mountain View, California
| | | | - Rick Tearle
- 5 Complete Genomics Inc, Mountain View, California.,7 Davies Research Centre, School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy, South Australia, Australia
| | - Andrew Stubbs
- 6 Department of Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
| | - James Harraway
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia
| | - Peter J van der Spek
- 6 Department of Bioinformatics, Erasmus MC, Rotterdam, The Netherlands.,8 Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Deon J Venter
- 1 Department of Pathology, Mater Health, South Brisbane, Queensland, Australia.,2 Mater Research Institute, University of Queensland, Queensland, Australia.,3 School of Medicine, University of Queensland, Queensland, Australia
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Hsueh PT, Wang HH, Liu CL, Ni WF, Chen YL, Liu JK. Expression of cerebral serotonin related to anxiety-like behaviors in C57BL/6 offspring induced by repeated subcutaneous prenatal exposure to low-dose lipopolysaccharide. PLoS One 2017. [PMID: 28650979 PMCID: PMC5484498 DOI: 10.1371/journal.pone.0179970] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Prenatal exposure to lipopolysaccharide (LPS), which likely occurs due to infection or contact with environmental allergens during pregnancy, is a proposed risk factor that induces anxiety- and autism spectrum disorder-like behaviors in offspring. However, the molecular and behavioral changes in offspring after maternal immune activation have not been completely identified. We hypothesized that a subcutaneous injection of LPS in a pregnant mouse would induce changes in cerebral serotonin (5-HT) in parallel to the appearance of anxiety-like behaviors in the dam’s offspring. After LPS injections (total, 100 μg/Kg), the time spent in the central region during the open field test and the number of times that the mice moved between the light and dark boxes and between the open and closed arms on the elevated plus maze test revealed anxiety-like behaviors in offspring at 5, 6 and 9 weeks of age. The mRNA expression levels of tph2 (5-HT synthesizing enzyme) and slc6a4 (5-HT transporter) were down-regulated in both adolescent (5 weeks of age) and adult (8 weeks of age) brains. Immunohistochemistry revealed that the numbers and sizes of tph2-expressing cells were notably decreased in the raphe nuclei of the midbrain of adults. Moreover, compared with controls (phosphate-buffered saline-treated offspring), the cerebral 5-HT concentration at adolescence and adulthood in LPS-induced offspring was significantly decreased. We concluded that maternal immune activation induced by exposure to a low dose of LPS decreased cerebral 5-HT levels in parallel to the down-regulation of the tph2 and slc6a4 genes and in conjunction with anxiety-like behaviors in offspring.
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Affiliation(s)
- Pei-Tan Hsueh
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hsuan-Han Wang
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Chiu-Lin Liu
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Wei-Fen Ni
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Ya-Lei Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
- * E-mail: (LJK); (CYL)
| | - Jong-Kang Liu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
- * E-mail: (LJK); (CYL)
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Quintela I, Eirís J, Gómez-Lado C, Pérez-Gay L, Dacruz D, Cruz R, Castro-Gago M, Míguez L, Carracedo Á, Barros F. Copy number variation analysis of patients with intellectual disability from North-West Spain. Gene 2017; 626:189-199. [PMID: 28506748 DOI: 10.1016/j.gene.2017.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/07/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
Intellectual disability (ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In the last decade, microarray-based copy number variation (CNV) analysis has been proved as a strategy particularly useful in the discovery of loci and candidate genes associated with these phenotypes and is widely used in the clinics with a diagnostic purpose. In this study, we evaluated the usefulness of two genome-wide high density SNP microarrays -Cytogenetics Whole-Genome 2.7M SNP array (n=126 patients; Group 1) and CytoScan High-Density SNP array (n=447 patients; Group 2)- in the detection of clinically relevant CNVs in a cohort of ID patients from Galicia (NW Spain). In 159 (27.7%) patients, we detected 186 rare exonic chromosomal imbalances, that were grouped into the following classes: Clinically relevant (67/186; 36.0%), of unknown clinical significance (93/186; 50.0%) and benign (26/186; 14.0%). The 67 pathogenic CNVs were identified in 64 patients, which means an overall diagnostic yield of 11.2%. Overall, we confirmed that ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide high density SNP microarrays in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with pathogenic or likely pathogenic CNVs and discussed the potential implication in neurodevelopmental disorders of genes located within these variants.
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Affiliation(s)
- Inés Quintela
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain
| | - Jesús Eirís
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Carmen Gómez-Lado
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Laura Pérez-Gay
- Hospital Universitario Lucus Augusti, Unidad de Neurología Pediátrica, Departamento de Pediatría, Lugo, Spain
| | - David Dacruz
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Raquel Cruz
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBER de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Santiago de Compostela, Spain
| | - Manuel Castro-Gago
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Luz Míguez
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain; King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia
| | - Francisco Barros
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain.
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Travan L, Naviglio S, De Cunto A, Pellegrin A, Pecile V, Spinelli AM, Cappellani S, Faletra F. Phenotypic expression of 19q13.32 microdeletions: Report of a new patient and review of the literature. Am J Med Genet A 2017; 173:1970-1974. [PMID: 28411391 DOI: 10.1002/ajmg.a.38256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 03/21/2017] [Indexed: 11/10/2022]
Abstract
The phenotypic manifestations of microdeletions in the 19q13.32 region are still poorly known. In this paper we report a patient who presented with hypotonia, developmental delay, facial dysmorphism, micrognathia, kyphoscoliosis, and buried penis. Chromosomal microarray revealed an interstitial 327 kb de novo microdeletion in the 19q13.32 region comprising eight genes (ARGHAP35, NPAS1, TMEM160, ZC3H4, SAE1, BBC3, MIR3190, and MIR3191). Previously reported cases of microdeletions in the 19q13.32 region were reviewed and compared to our patient, highlighting the common features of a possible 19q13.32 microdeletion syndrome.
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Affiliation(s)
- Laura Travan
- Department of Perinatal Medicine, Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Samuele Naviglio
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, Trieste, Italy
| | - Angela De Cunto
- Department of Perinatal Medicine, Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Andrea Pellegrin
- Department of Pediatric Radiology, Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Vanna Pecile
- Department of Genetics, Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | | | - Stefania Cappellani
- Department of Genetics, Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Flavio Faletra
- Department of Genetics, Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
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15
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Chromosomal microarray testing in adults with intellectual disability presenting with comorbid psychiatric disorders. Eur J Hum Genet 2016; 25:66-72. [PMID: 27650969 PMCID: PMC5159755 DOI: 10.1038/ejhg.2016.107] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/23/2016] [Accepted: 06/28/2016] [Indexed: 12/12/2022] Open
Abstract
Chromosomal copy-number variations (CNVs) are a class of genetic variants highly implicated in the aetiology of neurodevelopmental disorders, including intellectual disabilities (ID), schizophrenia and autism spectrum disorders (ASD). Yet the majority of adults with idiopathic ID presenting to psychiatric services have not been tested for CNVs. We undertook genome-wide chromosomal microarray analysis (CMA) of 202 adults with idiopathic ID recruited from community and in-patient ID psychiatry services across England. CNV pathogenicity was assessed using standard clinical diagnostic methods and participants underwent comprehensive medical and psychiatric phenotyping. We found an 11% yield of likely pathogenic CNVs (22/202). CNVs at recurrent loci, including the 15q11-q13 and 16p11.2-p13.11 regions were most frequently observed. We observed an increased frequency of 16p11.2 duplications compared with those reported in single-disorder cohorts. CNVs were also identified in genes known to effect neurodevelopment, namely NRXN1 and GRIN2B. Furthermore deletions at 2q13, 12q21.2-21.31 and 19q13.32, and duplications at 4p16.3, 13q32.3-33.3 and Xq24-25 were observed. Routine CMA in ID psychiatry could uncover ~11% new genetic diagnoses with potential implications for patient management. We advocate greater consideration of CMA in the assessment of adults with idiopathic ID presenting to psychiatry services.
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Nikkhah M, Rezazadeh M, Khorram Khorshid HR, Biglarian A, Ohadi M. An exceptionally long CA-repeat in the core promoter of SCGB2B2 links with the evolution of apes and Old World monkeys. Gene 2015; 576:109-14. [PMID: 26437309 DOI: 10.1016/j.gene.2015.09.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/31/2022]
Abstract
We have recently reported a genome-scale catalog of human protein-coding genes that contain "exceptionally long" STRs (≥6-repeats) in their core promoter, which may be of selective advantage in this species. At the top of that list, SCGB2B2 (also known as SCGBL), contains one of the longest CA-repeat STRs identified in a human gene core promoter, at 25-repeats. In the study reported here, we analyzed the conservation status of this CA-STR across evolution. The functional implication of this STR to alter gene expression activity was also analyzed in the HEK-293 cell line. We report that the SCGB2B2 core promoter CA-repeat reaches exceptional lengths, ranging from 9- to 25-repeats, across Apes (Hominoids) and the Old World monkeys (CA>2-repeats were not detected in any other species). The longest CA-repeats and highest identity in the SCGB2B2 protein sequence were observed between human and bonobo. A trend for increased gene expression activity was observed from the shorter to the longer CA-repeats (p<0.009), and the CA-repeat increased gene expression activity, per se (p<0.02). We propose that the SCGB2B2 gene core promoter CA-repeat functions as an expression code for the evolution of Apes and the Old World monkeys.
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Affiliation(s)
- M Nikkhah
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Rezazadeh
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Biglarian
- Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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