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Liu J, Wang Y, Zhao Y, Pan H, Liu Z, Xu Q, Lu S, Jiang H, Wang J, Sun Q, Tan J, Yan X, Li J, Tang B, Guo J. Comprehensive variant analysis of phospholipase A2 superfamily genes in large Chinese Parkinson' s disease cohorts. Mech Ageing Dev 2024; 219:111940. [PMID: 38750970 DOI: 10.1016/j.mad.2024.111940] [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: 01/16/2024] [Revised: 03/31/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024]
Abstract
To clarify the genetic role of phospholipase A2 (PLA2) genes in Parkinson's disease (PD), we performed a genetic association study in large Chinese population cohorts using next-generation sequencing. In this study, we analyzed both rare and common variants of 38 phospholipase A2 genes in two large cohorts. We detected 1558 and 1115 rare variants in these two cohorts, respectively. In both cohorts, we observed suggestive associations between specific subgroups and the risk of PD. At the single-gene level, several genes (PLA2G2D, PLA2G12A, PLA2G12B, PLA2G4F, PNPLA1, PNPLA3, PNPLA7, PLA2G7, PLA2G15, PLAAT5, and ABHD12) are suggestively associated with PD. Meanwhile, 364 and 2261 common variants were identified in two cohorts, respectively. Our study has expanded the genetic spectrum of the PLA2 family genes and suggested potential pathogenetic roles of PLA2 superfamily in PD.
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Affiliation(s)
- Jiabin Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shen Lu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jieqiong Tan
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
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Ruscu M, Capitanescu B, Rupek P, Dandekar T, Radu E, Hermann DM, Popa-Wagner A. The post-stroke young adult brain has limited capacity to re-express the gene expression patterns seen during early postnatal brain development. Brain Pathol 2024:e13232. [PMID: 38198833 DOI: 10.1111/bpa.13232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The developmental origins of the brain's response to injury can play an important role in recovery after a brain lesion. In this study, we investigated whether the ischemic young adult brain can re-express brain plasticity genes that were active during early postnatal development. Differentially expressed genes in the cortex of juvenile post-natal day 3 and the peri-infarcted cortical areas of young, 3-month-old post-stroke rats were identified using fixed-effects modeling within an empirical Bayes framework through condition-specific comparison. To further analyze potential biological processes, upregulated and downregulated genes were assessed for enrichment using GSEA software. The genes showing the highest expression changes were subsequently verified through RT-PCR. Our findings indicate that the adult brain partially recapitulates the gene expression profile observed in the juvenile brain but fails to upregulate many genes and pathways necessary for brain plasticity. Of the upregulated genes in post-stroke brains, specific roles have not been assigned to Apobec1, Cenpf, Ect2, Folr2, Glipr1, Myo1f, and Pttg1. New genes that failed to upregulate in the adult post-stroke brain include Bex4, Cd24, Klhl1/Mrp2, Trim67, and St8sia2. Among the upregulated pathways, the largest change was observed in the KEGG pathway "One carbon pool of folate," which is necessary for cellular proliferation, followed by the KEGG pathway "Antifolate resistance," whose genes mainly encode the family of ABC transporters responsible for the efflux of drugs that have entered the brain. We also noted three less-described downregulated KEGG pathways in experimental models: glycolipid biosynthesis, oxytocin, and cortisol pathways, which could be relevant as therapeutic targets. The limited brain plasticity of the adult brain is illustrated through molecular and histological analysis of the axonal growth factor, KIF4. Collectively, these results strongly suggest that further research is needed to decipher the complex genetic mechanisms that prevent the re-expression of brain plasticity-associated genes in the adult brain.
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Affiliation(s)
- Mihai Ruscu
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
| | | | - Paul Rupek
- Chair of Bioinformatics, University of Würzburg, Wuerzburg, Germany
| | - Thomas Dandekar
- Chair of Bioinformatics, University of Würzburg, Wuerzburg, Germany
| | - Eugen Radu
- University of Medicine and Pharmacy Carol Davila, Bucharest, Romania
| | - Dirk M Hermann
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
| | - Aurel Popa-Wagner
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
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Martínez-Rubio D, Hinarejos I, Argente-Escrig H, Marco-Marín C, Lozano MA, Gorría-Redondo N, Lupo V, Martí-Carrera I, Miranda C, Vázquez-López M, García-Pérez A, Marco-Hernández AV, Tomás-Vila M, Aguilera-Albesa S, Espinós C. Genetic Heterogeneity Underlying Phenotypes with Early-Onset Cerebellar Atrophy. Int J Mol Sci 2023; 24:16400. [PMID: 38003592 PMCID: PMC10671053 DOI: 10.3390/ijms242216400] [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: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Cerebellar atrophy (CA) is a frequent neuroimaging finding in paediatric neurology, usually associated with cerebellar ataxia. The list of genes involved in hereditary forms of CA is continuously growing and reveals its genetic complexity. We investigated ten cases with early-onset cerebellar involvement with and without ataxia by exome sequencing or by a targeted panel with 363 genes involved in ataxia or spastic paraplegia. Novel variants were investigated by in silico or experimental approaches. Seven probands carry causative variants in well-known genes associated with CA or cerebellar hypoplasia: SETX, CACNA1G, CACNA1A, CLN6, CPLANE1, and TBCD. The remaining three cases deserve special attention; they harbour variants in MAST1, PI4KA and CLK2 genes. MAST1 is responsible for an ultrarare condition characterised by global developmental delay and cognitive decline; our index case added ataxia to the list of concomitant associated symptoms. PIK4A is mainly related to hypomyelinating leukodystrophy; our proband presented with pure spastic paraplegia and normal intellectual capacity. Finally, in a patient who suffers from mild ataxia with oculomotor apraxia, the de novo novel CLK2 c.1120T>C variant was found. The protein expression of the mutated protein was reduced, which may indicate instability that would affect its kinase activity.
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Affiliation(s)
- Dolores Martínez-Rubio
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
- Joint Unit CIPF-IIS La Fe Rare Diseases, 46012 València, Spain
| | - Isabel Hinarejos
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
- Joint Unit CIPF-IIS La Fe Rare Diseases, 46012 València, Spain
| | | | - Clara Marco-Marín
- Structural Enzymopathology Unit, Instituto de Biomedicina de Valencia (IBV), Consejo Superior de Investigaciones Científicas (CSIC), 46022 València, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - María Ana Lozano
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
| | - Nerea Gorría-Redondo
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario de Navarra, Navarrabiomed, 31008 Pamplona, Spain
| | - Vincenzo Lupo
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
| | - Itxaso Martí-Carrera
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario Donostia, 20014 Donostia, Spain
| | - Concepción Miranda
- Paediatric Neurology Unit, Department of Paediatrics, Hospital General Universitario Gregorio Marañón, 28027 Madrid, Spain
| | - María Vázquez-López
- Paediatric Neurology Unit, Department of Paediatrics, Hospital General Universitario Gregorio Marañón, 28027 Madrid, Spain
| | - Asunción García-Pérez
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - Ana Victoria Marco-Hernández
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitari Doctor, Peset, 46017 València, Spain
| | - Miguel Tomás-Vila
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitari i Politècnic La Fe, 46026 València, Spain
| | - Sergio Aguilera-Albesa
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario de Navarra, Navarrabiomed, 31008 Pamplona, Spain
| | - Carmen Espinós
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
- Joint Unit CIPF-IIS La Fe Rare Diseases, 46012 València, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
- Biotechnology Department, Universitat Politècnica de València, 46022 València, Spain
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Smirnov D, Konstantinovskiy N, Prokisch H. Integrative omics approaches to advance rare disease diagnostics. J Inherit Metab Dis 2023; 46:824-838. [PMID: 37553850 DOI: 10.1002/jimd.12663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
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Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Nikita Konstantinovskiy
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
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Huang Z, Merrihew GE, Larson EB, Park J, Plubell D, Fox EJ, Montine KS, Latimer CS, Dirk Keene C, Zou JY, MacCoss MJ, Montine TJ. Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer's disease. Nat Commun 2023; 14:2747. [PMID: 37173305 PMCID: PMC10182086 DOI: 10.1038/s41467-023-38376-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Resilience to Alzheimer's disease is an uncommon combination of high disease burden without dementia that offers valuable insights into limiting clinical impact. Here we assessed 43 research participants meeting stringent criteria, 11 healthy controls, 12 resilience to Alzheimer's disease and 20 Alzheimer's disease with dementia and analyzed matched isocortical regions, hippocampus, and caudate nucleus by mass spectrometry-based proteomics. Of 7115 differentially expressed soluble proteins, lower isocortical and hippocampal soluble Aβ levels is a significant feature of resilience when compared to healthy control and Alzheimer's disease dementia groups. Protein co-expression analysis reveals 181 densely-interacting proteins significantly associated with resilience that were enriched for actin filament-based processes, cellular detoxification, and wound healing in isocortex and hippocampus, further supported by four validation cohorts. Our results suggest that lowering soluble Aβ concentration may suppress severe cognitive impairment along the Alzheimer's disease continuum. The molecular basis of resilience likely holds important therapeutic insights.
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Affiliation(s)
- Zhi Huang
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gennifer E Merrihew
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Eric B Larson
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Deanna Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Edward J Fox
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Caitlin S Latimer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - James Y Zou
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Domínguez-Sala E, Valdés-Sánchez L, Canals S, Reiner O, Pombero A, García-López R, Estirado A, Pastor D, Geijo-Barrientos E, Martínez S. Abnormalities in Cortical GABAergic Interneurons of the Primary Motor Cortex Caused by Lis1 (Pafah1b1) Mutation Produce a Non-drastic Functional Phenotype. Front Cell Dev Biol 2022; 10:769853. [PMID: 35309904 PMCID: PMC8924048 DOI: 10.3389/fcell.2022.769853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
LIS1 (PAFAH1B1) plays a major role in the developing cerebral cortex, and haploinsufficient mutations cause human lissencephaly type 1. We have studied morphological and functional properties of the cerebral cortex of mutant mice harboring a deletion in the first exon of the mouse Lis1 (Pafah1b1) gene, which encodes for the LisH domain. The Lis1/sLis1 animals had an overall unaltered cortical structure but showed an abnormal distribution of cortical GABAergic interneurons (those expressing calbindin, calretinin, or parvalbumin), which mainly accumulated in the deep neocortical layers. Interestingly, the study of the oscillatory activity revealed an apparent inability of the cortical circuits to produce correct activity patterns. Moreover, the fast spiking (FS) inhibitory GABAergic interneurons exhibited several abnormalities regarding the size of the action potentials, the threshold for spike firing, the time course of the action potential after-hyperpolarization (AHP), the firing frequency, and the frequency and peak amplitude of spontaneous excitatory postsynaptic currents (sEPSC’s). These morphological and functional alterations in the cortical inhibitory system characterize the Lis1/sLis1 mouse as a model of mild lissencephaly, showing a phenotype less drastic than the typical phenotype attributed to classical lissencephaly. Therefore, the results described in the present manuscript corroborate the idea that mutations in some regions of the Lis1 gene can produce phenotypes more similar to those typically described in schizophrenic and autistic patients and animal models.
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Affiliation(s)
- E Domínguez-Sala
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - L Valdés-Sánchez
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - S Canals
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - O Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - A Pombero
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - R García-López
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - A Estirado
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - D Pastor
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - E Geijo-Barrientos
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain
| | - S Martínez
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Sant Joan d'Alacant, Spain.,Centro de Investigación Biomédica en Red en Salud Mental CIBERSAM, Madrid, Spain
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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Shen P, Xu A, Hou Y, Wang H, Gao C, He F, Yang D. Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics. BMC Mol Cell Biol 2021; 22:7. [PMID: 33482715 PMCID: PMC7821633 DOI: 10.1186/s12860-021-00346-w] [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: 09/20/2020] [Accepted: 01/13/2021] [Indexed: 12/03/2022] Open
Abstract
Background One striking feature of the large KRAB domain-containing zinc finger protein (KZFP) family is its rapid evolution, leading to hundreds of member genes with various origination time in a certain mammalian genome. However, a comprehensive genome-wide and across-taxa analysis of the structural and expressional features of KZFPs with different origination time is lacking. This type of analysis will provide valuable clues about the functional characteristics of this special family. Results In this study, we found several conserved paradoxical phenomena about this issue. 1) Ordinary young domains/proteins tend to be disordered, but most of KRAB domains are completely structured in 64 representative species across the superclass of Sarcopterygii and most of KZFPs are also highly structured, indicating their rigid and unique structural and functional characteristics; as exceptions, old-zinc-finger-containing KZFPs have relatively disordered KRAB domains and linker regions, contributing to diverse interacting partners and functions. 2) In general, young or highly structured proteins tend to be spatiotemporal specific and have low abundance. However, by integrated analysis of 29 RNA-seq datasets, including 725 samples across early embryonic development, embryonic stem cell differentiation, embryonic and adult organs, tissues in 7 mammals, we found that KZFPs tend to express ubiquitously with medium abundance regardless of evolutionary age and structural disorder degree, indicating the wide functional requirements of KZFPs in various states. 3) Clustering and correlation analysis reveal that there are differential expression patterns across different spatiotemporal states, suggesting the specific-high-expression KZFPs may play important roles in the corresponding states. In particular, part of young-zinc-finger-containing KZFPs are highly expressed in early embryonic development and ESCs differentiation into endoderm or mesoderm. Co-expression analysis revealed that young-zinc-finger-containing KZFPs are significantly enriched in five co-expression modules. Among them, one module, including 13 young-zinc-finger-containing KZFPs, showed an ‘early-high and late-low’ expression pattern. Further functional analysis revealed that they may function in early embryonic development and ESC differentiation via participating in cell cycle related processes. Conclusions This study shows the conserved and special structural, expressional features of KZFPs, providing new clues about their functional characteristics and potential causes of their rapid evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00346-w.
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Affiliation(s)
- Pan Shen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Aishi Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.,Animal Sciences College of Jilin University, Changchun, 130062, China
| | - Yushan Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Huqiang Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Chao Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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Xi H, Peng Y, Xie W, Pang J, Ma N, Yang S, Peng J, Wang H. A chromosome 1q22 microdeletion including ASH1L is associated with intellectual disability in a Chinese family. Mol Cytogenet 2020; 13:20. [PMID: 32518592 PMCID: PMC7273683 DOI: 10.1186/s13039-020-00483-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/27/2020] [Indexed: 01/18/2023] Open
Abstract
Background Copy number variants (CNVs) associated with developmental delay and intellectual disability (DD/ID) continue to be identified in patients. This article reports identification of a chromosome 1q22 microdeletion as the genetic cause in a Chinese family affected by ID. Case presentation The proband was a 19-year-old pregnant woman referred for genetic counseling and prenatal diagnosis at 18 weeks of gestation. She had severe ID with basically normal stature (height 154 cm [0 SD], weight 61 kg [− 0.2 SD], and head circumference 54 cm [− 1.12 SD]). Her distinctive facial features included a prominent forehead; flat face; flat nasal bridge and a short upturned nose; thin lips; and small ears. The proband’s father was reported to have low intelligence, whereas her mother was of normal intelligence but with scoliosis. Chromosome microarray analysis (CMA) reveals that the proband, her father and the fetus all carry a 1q22 microdeletion of 936.3 Kb (arr[GRCh37] 1q22 (155016052_155952375)×1), which was not observed in her mother and paternal grandparents and uncles, suggesting a de novo mutation in the proband’s father. The microdeletion involves 24 OMIM genes including ASH1L (also known as KMT2H and encoding a histone lysine methyltransferase). Of note, haploinsufficiency of ASH1L has been shown to be associated with neurodevelopmental disorders. Based on the inheritance of the detected CNV in the pedigree and similar CNVs associated with ID in public databases (Decipher, DGV and ClinVar) and literature, the detected CNV is considered as pathogenic. The family chose to terminate the pregnancy. Conclusions The identified 1q22 microdeletion including ASH1L is pathogenic and associated with ID. This case broadens the spectrum of ID-related CNVs and may be useful as a reference for clinicians.
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Affiliation(s)
- Hui Xi
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Ying Peng
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Wanqin Xie
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Jialun Pang
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Na Ma
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Shuting Yang
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
| | - Jinping Peng
- Department of Medical Genetics, Maternal and Child Health Care Hospital of Shaoyang City, Shaoyang, Hunan Province P. R. China
| | - Hua Wang
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China.,The Prenatal Diagnosis Center of Hunan Province, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan Province P. R. China
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10
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Murcia Pienkowski V, Kucharczyk M, Rydzanicz M, Poszewiecka B, Pachota K, Młynek M, Stawiński P, Pollak A, Kosińska J, Wojciechowska K, Lejman M, Cieślikowska A, Wicher D, Stembalska A, Matuszewska K, Materna-Kiryluk A, Gambin A, Chrzanowska K, Krajewska-Walasek M, Płoski R. Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype. J Clin Med 2020; 9:jcm9051245. [PMID: 32344861 PMCID: PMC7287862 DOI: 10.3390/jcm9051245] [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: 03/26/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
De novo balanced chromosomal aberrations (BCAs), such as reciprocal translocations and inversions, are genomic aberrations that, in approximately 25% of cases, affect the human phenotype. Delineation of the exact structure of BCAs may provide a precise diagnosis and/or point to new disease loci. We report on six patients with de novo balanced chromosomal translocations (BCTs) and one patient with a de novo inversion, in whom we mapped breakpoints to a resolution of 1 bp, using shallow whole-genome mate pair sequencing. In all seven cases, a disruption of at least one gene was found. In two patients, the phenotypic impact of the disrupted genes is well known (NFIA, ATP7A). In five patients, the aberration damaged genes: PARD3, EPHA6, KLF13, STK24, UBR3, MLLT10 and TLE3, whose influence on the human phenotype is poorly understood. In particular, our results suggest novel candidate genes for retinal degeneration with anophthalmia (EPHA6), developmental delay with speech impairment (KLF13), and developmental delay with brain dysembryoplastic neuroepithelial tumor (UBR3). In conclusion, identification of the exact structure of symptomatic BCTs using next generation sequencing is a viable method for both diagnosis and finding novel disease candidate genes in humans.
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Affiliation(s)
- Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Barbara Poszewiecka
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Katarzyna Pachota
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Marlena Młynek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Katarzyna Wojciechowska
- Department of Pediatric Hematology Oncology and Transplantology, University Children’s Hospital, 20-093 Lublin, Poland;
| | - Monika Lejman
- Department of Pediatric Hematology Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Agata Cieślikowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Dorota Wicher
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | | | - Karolina Matuszewska
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Gambin
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Krajewska-Walasek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
- Correspondence: ; Tel.: +48-22-572-06-95; Fax: +48-22-572-06-96
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11
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Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS One 2019; 14:e0223337. [PMID: 31577830 PMCID: PMC6774566 DOI: 10.1371/journal.pone.0223337] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5-35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as having diagnostic, prognostic or therapeutic relevance. Isolated reports exist of fusion transcripts being detected in cases of developmental and neurological phenotypes, and thus, systematic application of fusion detection to germline conditions may further increase diagnostic rates. However, current fusion detection methods are unsuited to the investigation of germline disease due to performance biases arising from their development using tumor, cell-line or in-silico data. METHODS We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering steps, and instead, prioritize candidates using a custom workflow that integrates genomic and transcriptomic sequence alignment, biological and technical annotations, customized categorization logic, and phenotypic prioritization. RESULTS We demonstrate that our approach to fusion transcript identification and prioritization detects genuine fusion events excluded by standard analyses and efficiently removes phenotypically unimportant candidates and false positive events, resulting in a reduced candidate list enriched for events with potential phenotypic relevance. We describe the successful genetic resolution of two previously undiagnosed disease cases through the detection of pathogenic fusion transcripts. Furthermore, we report the experimental validation of five additional cases of fusion transcripts with potential phenotypic relevance. CONCLUSIONS The approach we describe can be implemented to enable the detection of phenotypically relevant fusion transcripts in studies of rare inherited disease. Fusion transcript detection has the potential to increase diagnostic rates in rare inherited disease and should be included in RNA-based analytical pipelines aimed at genetic diagnosis.
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Affiliation(s)
- Gavin R. Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Laura E. Schultz-Rogers
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - W. Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Krutika Gaonkar
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Pritha Chanana
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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12
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Singh A, Zahra S, Das D, Kumar S. AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5277248. [PMID: 30624648 PMCID: PMC6323297 DOI: 10.1093/database/bay135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/29/2018] [Indexed: 02/02/2023]
Abstract
Fusion transcripts are chimeric RNAs generated as a result of fusion either at DNA or RNA level. These novel transcripts have been extensively studied in the case of human cancers but still remain underexamined in plants. In this study, we introduce the first plant-specific database of fusion transcripts named AtFusionDB (http://www.nipgr.res.in/AtFusionDB). This is a comprehensive database that contains the detailed information about fusion transcripts identified in model plant Arabidopsis thaliana. A total of 82 969 fusion transcript entries generated from 17 181 different genes of A. thaliana are available in this database. Apart from the basic information consisting of the Ensembl gene names, official gene name, tissue type, EricScore, fusion type, AtFusionDB ID and sample ID (e.g. Sequence Read Archive ID), additional information like UniProt, gene coordinates (together with the function of parental genes), junction sequence, expression level of both parent genes and fusion transcript may be of high utility to the user. Two different types of search modules viz. ‘Simple Search’ and ‘Advanced Search’ in addition to the ‘Browse’ option with data download facility are provided in this database. Three different modules for mapping and alignment of the query sequences viz. BLASTN, SW Align and Mapping are incorporated in AtFusionDB. This database is a head start for exploring the complex and unexplored domain of gene/transcript fusion in plants.
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Affiliation(s)
- Ajeet Singh
- Bioinformatics Laboratory, National Institute of Plant Genome Research Aruna Asaf Ali Marg, New Delhi, India
| | - Shafaque Zahra
- Bioinformatics Laboratory, National Institute of Plant Genome Research Aruna Asaf Ali Marg, New Delhi, India
| | - Durdam Das
- Bioinformatics Laboratory, National Institute of Plant Genome Research Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research Aruna Asaf Ali Marg, New Delhi, India
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13
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Murcia Pienkowski V, Kucharczyk M, Młynek M, Szczałuba K, Rydzanicz M, Poszewiecka B, Skórka A, Sykulski M, Biernacka A, Koppolu AA, Posmyk R, Walczak A, Kosińska J, Krajewski P, Castaneda J, Obersztyn E, Jurkiewicz E, Śmigiel R, Gambin A, Chrzanowska K, Krajewska-Walasek M, Płoski R. Mapping of breakpoints in balanced chromosomal translocations by shallow whole-genome sequencing points to EFNA5, BAHD1 and PPP2R5E as novel candidates for genes causing human Mendelian disorders. J Med Genet 2018; 56:104-112. [PMID: 30352868 DOI: 10.1136/jmedgenet-2018-105527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mapping the breakpoints in de novo balanced chromosomal translocations (BCT) in symptomatic individuals provides a unique opportunity to identify in an unbiased way the likely causative genetic defect and thus find novel human disease candidate genes. Our aim was to fine-map breakpoints of de novo BCTs in a case series of nine patients. METHODS Shallow whole-genome mate pair sequencing (SGMPS) together with long-range PCR and Sanger sequencing. In one case (BCT disrupting BAHD1 and RET) cDNA analysis was used to verify expression of a fusion transcript in cultured fibroblasts. RESULTS In all nine probands 11 disrupted genes were found, that is, EFNA5, EBF3, LARGE, PPP2R5E, TXNDC5, ZNF423, NIPBL, BAHD1, RET, TRPS1 and SLC4A10. Five subjects had translocations that disrupted genes with so far unknown (EFNA5, BAHD1, PPP2R5E, TXNDC5) or poorly delineated impact on the phenotype (SLC4A10, two previous reports of BCT disrupting the gene). The four genes with no previous disease associations (EFNA5, BAHD1, PPP2R5E, TXNDC5), when compared with all human genes by a bootstrap test, had significantly higher pLI (p<0.017) and DOMINO (p<0.02) scores indicating enrichment in genes likely to be intolerant to single copy damage. Inspection of individual pLI and DOMINO scores, and local topologically associating domain structure suggested that EFNA5, BAHD1 and PPP2R5E were particularly good candidates for novel disease loci. The pathomechanism for BAHD1 may involve deregulation of expression due to fusion with RET promoter. CONCLUSION SGMPS in symptomatic carriers of BCTs is a powerful approach to delineate novel human gene-disease associations.
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Affiliation(s)
- Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marlena Młynek
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Barbara Poszewiecka
- Faculty of Mathematics, Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Agata Skórka
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland.,Department of Pediatrics, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Sykulski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,genXone, Poznan, Poland
| | - Anna Biernacka
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Anna Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Renata Posmyk
- Department of Clinical Genetics, Podlaskie Medical Center, Bialystok, Poland.,Department of Perinatology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Paweł Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Jennifer Castaneda
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Elżbieta Jurkiewicz
- Department of Diagnostic Imaging, The Children's Memorial Health Institute, Warsaw, Poland
| | - Robert Śmigiel
- Department of Pediatrics and Rare Disorder, Wroclaw Medical University, Wroclaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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14
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Canet-Pons J, Schubert R, Duecker RP, Schrewe R, Wölke S, Kieslich M, Schnölzer M, Chiocchetti A, Auburger G, Zielen S, Warnken U. Ataxia telangiectasia alters the ApoB and reelin pathway. Neurogenetics 2018; 19:237-255. [DOI: 10.1007/s10048-018-0557-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023]
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15
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Kono N, Arai H. Platelet-activating factor acetylhydrolases: An overview and update. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:922-931. [PMID: 30055287 DOI: 10.1016/j.bbalip.2018.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/19/2018] [Accepted: 07/23/2018] [Indexed: 01/22/2023]
Abstract
Platelet-activating factor acetylhydrolases (PAF-AHs) are unique members of the phospholipase A2 family that can hydrolyze the acetyl group of PAF, a signaling phospholipid that has roles in diverse (patho)physiological processes. Three types of PAF-AH have been identified in mammals, one plasma type and two intracellular types [PAF-AH (I) and PAF-AH (II)]. Plasma PAF-AH and PAF-AH (II) are monomeric enzymes that are structurally similar, while PAF-AH (I) is a multimeric enzyme with no homology to other PAF-AHs. PAF-AH (I) shows a strong preference for an acetyl group, whereas plasma PAF-AH and PAF-AH (II) also hydrolyze phospholipids with oxidatively modified fatty acids. Plasma PAF-AH has been implicated in several diseases including cardiovascular disease. PAF-AH (I) is required for spermatogenesis and is increasingly recognized as an oncogenic factor. PAF-AH (II) was recently shown to act as a bioactive lipid-producing enzyme in mast cells and thus could be a drug target for allergic diseases. This article is part of a Special Issue entitled Novel functions of phospholipase A2 Guest Editors: Makoto Murakami and Gerard Lambeau.
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Affiliation(s)
- Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; PRIME, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyodaku, Tokyo 100-0004, Japan.
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyodaku, Tokyo 100-0004, Japan
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16
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Abstract
We report on three nonrelated patients with intellectual disability and CNVs that give rise to three new chimeric genes. All the genes forming these fusion transcripts may have an important role in central nervous system development and/or in gene expression regulation, and therefore not only their deletion or duplication but also the resulting chimeric gene may contribute to the phenotype of the patients. Deletions and duplications are usually pathogenic when affecting dose-sensitive genes. Alternatively, a chimeric gene may also be pathogenic by different gain-of-function mechanisms that are not restricted to dose-sensitive genes: the emergence of a new polypeptide that combines functional domains from two different genes, the deregulated expression of any coding sequence by the promoter region of a neighboring gene, and/or a putative dominant-negative effect due to the preservation of functional domains of partially truncated proteins. Fusion oncogenes are well known, but in other pathologies, the search for chimeric genes is disregarded. According to our findings, we hypothesize that the frequency of fusion transcripts may be much higher than suspected, and it should be taken into account in the array-CGH analyses of patients with intellectual disability.
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17
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Wilms V, Söffgen C, Nothwang HG. Differences in molecular mechanisms of K+ clearance in the auditory sensory epithelium of birds and mammals. J Exp Biol 2017; 220:2701-2705. [DOI: 10.1242/jeb.158030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022]
Abstract
Mechanoelectrical transduction in the vertebrate inner ear is a highly conserved mechanism depending on K+ influx into hair cells. Here, we investigated the molecular underpinnings of subsequent K+ recycling in the chicken basilar papilla and compared it with those in the mammalian auditory sensory epithelium. Like mammals, the avian auditory hair cell uses KCNQ4, KCNMA1, and KCNMB1 as K+ efflux systems. Expression of KCNQ1 and KCNE1 suggests an additional efflux apparatus in avian hair cells. Marked differences were observed for K+ clearance. In mammals, KCC3, KCC4, Kir4.1, and CLC-K are present in supporting cells. Of these proteins, only CLC-K is expressed in avian supporting cells. Instead, they possess NKCC1 to move K+ across the membrane. This expression pattern suggests an avian clearance mechanism reminiscent of the well-established K+ uptake apparatus present in inner ear secretory cells. Altogether, tetrapod hair cells show similar mechanisms and supporting cells distinct molecular underpinnings of K+ recycling.
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Affiliation(s)
- Viviane Wilms
- Neurogenetics group, Cluster of Excellence “Hearing4All”, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
| | - Chris Söffgen
- Neurogenetics group, Cluster of Excellence “Hearing4All”, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
| | - Hans Gerd Nothwang
- Neurogenetics group, Cluster of Excellence “Hearing4All”, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
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18
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Prak K, Kriston-Vizi J, Chan AWE, Luft C, Costa JR, Pengo N, Ketteler R. Benzobisthiazoles Represent a Novel Scaffold for Kinase Inhibitors of CLK Family Members. Biochemistry 2016; 55:608-17. [PMID: 26701387 PMCID: PMC4730229 DOI: 10.1021/acs.biochem.5b01128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Protein kinases are essential regulators
of most cellular processes
and are involved in the etiology and progression of multiple diseases.
The cdc2-like kinases (CLKs) have been linked to various neurodegenerative
disorders, metabolic regulation, and virus infection, and the kinases
have been recognized as potential drug targets. Here, we have developed
a screening workflow for the identification of potent CLK2 inhibitors
and identified compounds with a novel chemical scaffold structure,
the benzobisthiazoles, that has not been previously reported for kinase
inhibitors. We propose models for binding of these compounds to CLK
family proteins and key residues in CLK2 that are important for the
compound interactions and the kinase activity. We identified structural
elements within the benzobisthiazole that determine CLK2 and CLK3
inhibition, thus providing a rationale for selectivity assays. In
summary, our results will inform structure-based design of CLK family
inhibitors based on the novel benzobisthiazole scaffold.
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Affiliation(s)
- Krisna Prak
- MRC Laboratory for Molecular Cell Biology, University College London , London WC1E 6BT, U.K
| | - Janos Kriston-Vizi
- MRC Laboratory for Molecular Cell Biology, University College London , London WC1E 6BT, U.K
| | - A W Edith Chan
- Wolfson Institute for Biomedical Research, University College London , London WC1E 6BT, U.K
| | - Christin Luft
- MRC Laboratory for Molecular Cell Biology, University College London , London WC1E 6BT, U.K
| | - Joana R Costa
- MRC Laboratory for Molecular Cell Biology, University College London , London WC1E 6BT, U.K
| | - Niccolo Pengo
- MRC Laboratory for Molecular Cell Biology, University College London , London WC1E 6BT, U.K
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London , London WC1E 6BT, U.K
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19
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Abstract
Platelet-activating factor (PAF) is a phospholipid mediator whose synthesis and degradation depend on specific sets of enzymes. PAF-acetylhydrolase (PAF-AH) hydrolyzes the acetyl moiety of PAF at its sn-2 position and thereby inactivates it. PAF-AH Ib, originally identified in brain, exists in the cytoplasm of many (probably all) types of mammalian cells and tissues. PAF-AH Ib consists of three subunits (α1, α2, and β), in which the α subunits provide the catalytic activity. The finding that the β subunit is the product of the causative gene for Miller-Dieker lissencephaly led to extensive analyses of PAF-AH Ib subunits in the field of cell biology and neurobiology. More than 20 molecules are known to bind to PAF-AH Ib subunits, and PAF-AH Ib has been implicated in neuronal development, neuronal functions, Alzheimer's disease, bipolar disorder, cancer, spermatogenesis, and tolerance to hypoxia. However, in almost all of these cases, how the catalytic activity is involved and the identity of the most important substrate of this enzyme are unclear. In this chapter, the structure and functions of PAF-AH Ib and its subunit proteins are summarized and their contributions to human diseases are discussed.
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Affiliation(s)
- Mitsuharu Hattori
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, the University of Tokyo, Tokyo, Japan.
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20
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Poot M. Gene Fusion due to Chromosome Misconnection May Seriously Affect Your Health. Mol Syndromol 2015; 6:55-7. [PMID: 26279648 DOI: 10.1159/000381081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2015] [Indexed: 11/19/2022] Open
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21
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Poot M, Haaf T. Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements. Mol Syndromol 2015; 6:110-34. [PMID: 26732513 DOI: 10.1159/000438812] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 01/08/2023] Open
Abstract
Complex chromosome rearrangements (CCRs) are currently defined as structural genome variations that involve more than 2 chromosome breaks and result in exchanges of chromosomal segments. They are thought to be extremely rare, but their detection rate is rising because of improvements in molecular cytogenetic technology. Their population frequency is also underestimated, since many CCRs may not elicit a phenotypic effect. CCRs may be the result of fork stalling and template switching, microhomology-mediated break-induced repair, breakage-fusion-bridge cycles, or chromothripsis. Patients with chromosomal instability syndromes show elevated rates of CCRs due to impaired DNA double-strand break responses during meiosis. Therefore, the putative functions of the proteins encoded by ATM, BLM, WRN, ATR, MRE11, NBS1, and RAD51 in preventing CCRs are discussed. CCRs may exert a pathogenic effect by either (1) gene dosage-dependent mechanisms, e.g. haploinsufficiency, (2) mechanisms based on disruption of the genomic architecture, such that genes, parts of genes or regulatory elements are truncated, fused or relocated and thus their interactions disturbed - these mechanisms will predominantly affect gene expression - or (3) mixed mutation mechanisms in which a CCR on one chromosome is combined with a different type of mutation on the other chromosome. Such inferred mechanisms of pathogenicity need corroboration by mRNA sequencing. Also, future studies with in vitro models, such as inducible pluripotent stem cells from patients with CCRs, and transgenic model organisms should substantiate current inferences regarding putative pathogenic effects of CCRs. The ramifications of the growing body of information on CCRs for clinical and experimental genetics and future treatment modalities are briefly illustrated with 2 cases, one of which suggests KDM4C (JMJD2C) as a novel candidate gene for mental retardation.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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22
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Disruption of NCOA2 by recurrent fusion with LACTB2 in colorectal cancer. Oncogene 2015; 35:187-95. [PMID: 25823027 PMCID: PMC4717154 DOI: 10.1038/onc.2015.72] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 12/19/2022]
Abstract
Whole-genome and transcriptome sequencing were used to discover novel gene fusions in a case of colon cancer. A tumor-specific LACTB2-NCOA2 fusion originating from intra-chromosomal rearrangement of chromosome 8 was identified at both DNA and RNA levels. Unlike conventional oncogenic chimeric proteins, the fusion product lacks functional domain from respective genes, indicative of an amorphic rearrangement. This chimeric LACTB2-NCOA2 transcript was detected in 6 out of 99 (6.1%) colorectal cancer (CRC) cases, where NCOA2 was significantly downregulated. Enforced expression of wild-type NCOA2 but not the LACTB2-NCOA2 fusion protein impaired the pro-tumorigenic phenotypes of CRC cells, whereas knockdown of endogenous NCOA2 in normal colonocytes had opposite effects. Mechanistically, NCOA2 inhibited Wnt/β-catenin signaling through simultaneously upregulating inhibitors and downregulating stimulators of Wnt/β-catenin pathway. Collectively, our data supports that NCOA2 is a novel negative growth regulatory gene repressing the Wnt/β-catenin pathway in CRC, where recurrent fusion with LACTB2 contributes to its disruption.
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23
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Bertelsen B, Melchior L, Jensen LR, Groth C, Nazaryan L, Debes NM, Skov L, Xie G, Sun W, Brøndum-Nielsen K, Kuss AW, Chen W, Tümer Z. A t(3;9)(q25.1;q34.3) translocation leading to OLFM1 fusion transcripts in Gilles de la Tourette syndrome, OCD and ADHD. Psychiatry Res 2015; 225:268-75. [PMID: 25595337 DOI: 10.1016/j.psychres.2014.12.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/08/2014] [Accepted: 12/18/2014] [Indexed: 01/13/2023]
Abstract
Gilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder with a strong genetic etiology; however, finding of candidate genes is hampered by its genetic heterogeneity and the influence of non-genetic factors on disease pathogenesis. We report a case of a male patient with GTS, obsessive compulsive disorder, attention-deficit/hyperactivity-disorder, as well as other comorbidities, and a translocation t(3;9)(q25.1;q34.3) inherited from a mother with tics. Mate-pair sequencing revealed that the translocation breakpoints truncated the olfactomedin 1 (OLFM1) gene and two uncharacterized transcripts. Reverse-transcription PCR identified several fusion transcripts in the carriers, and OLFM1 expression was found to be high in GTS-related human brain regions. As OLFM1 plays a role in neuronal development it is a likely candidate gene for neuropsychiatric disorders and haploinsufficiency of OLFM1 could be a contributing risk factor to the phenotype of the carriers. In addition, one of the fusion transcripts may exert a dominant-negative or gain-of-function effect. OLFM1 is unlikely to be a major GTS susceptibility gene as no point mutations or copy number variants affecting OLFM1 were identified in 175 additional patients. The translocation described is thus a unique event, but further studies in larger cohorts are required to elucidate involvement of OLFM1 in GTS pathogenesis.
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Affiliation(s)
- Birgitte Bertelsen
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Linea Melchior
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Lars Riff Jensen
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Camilla Groth
- Tourette Clinic, Department of Pediatrics, Copenhagen University Hospital, Herlev Hospital, Herlev, Denmark
| | - Lusine Nazaryan
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Nanette Mol Debes
- Tourette Clinic, Department of Pediatrics, Copenhagen University Hospital, Herlev Hospital, Herlev, Denmark
| | - Liselotte Skov
- Tourette Clinic, Department of Pediatrics, Copenhagen University Hospital, Herlev Hospital, Herlev, Denmark
| | - Gangcai Xie
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Wei Sun
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Karen Brøndum-Nielsen
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Andreas Walter Kuss
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Wei Chen
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Zeynep Tümer
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark.
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24
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Karasawa K, Inoue K. Overview of PAF-Degrading Enzymes. PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES (PAF-AH) 2015; 38:1-22. [DOI: 10.1016/bs.enz.2015.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Kloosterman WP, Hochstenbach R. Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease. Mol Cytogenet 2014; 7:100. [PMID: 25606056 PMCID: PMC4299681 DOI: 10.1186/s13039-014-0100-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/08/2014] [Indexed: 01/14/2023] Open
Abstract
Chromosomal aberrations include translocations, deletions, duplications, inversions, aneuploidies and complex rearrangements. They underlie genetic disease in roughly 15% of patients with multiple congenital abnormalities and/or mental retardation (MCA/MR). In genetic diagnostics, the pathogenicity of chromosomal aberrations in these patients is typically assessed based on criteria such as phenotypic similarity to other patients with the same or overlapping aberration, absence in healthy individuals, de novo occurrence, and protein coding gene content. However, a thorough understanding of the molecular mechanisms that lead to MCA/MR as a result of chromosome aberrations is often lacking. Chromosome aberrations can affect one or more genes in a complex manner, such as by changing the regulation of gene expression, by disrupting exons, and by creating fusion genes. The precise delineation of breakpoints by whole-genome sequencing enables the construction of local genomic architecture and facilitates the prediction of the molecular determinants of the patient's phenotype. Here, we review current methods for breakpoint identification and their impact on the interpretation of chromosome aberrations in patients with MCA/MR. In addition, we discuss opportunities to dissect disease mechanisms based on large-scale genomic technologies and studies in model organisms.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, P.O. Box 85060, 3508 AB Utrecht, The Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Genome Diagnostics, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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26
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Ponsuksili S, Murani E, Trakooljul N, Schwerin M, Wimmers K. Discovery of candidate genes for muscle traits based on GWAS supported by eQTL-analysis. Int J Biol Sci 2014; 10:327-37. [PMID: 24643240 PMCID: PMC3957088 DOI: 10.7150/ijbs.8134] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/22/2014] [Indexed: 12/12/2022] Open
Abstract
Biochemical and biophysical processes that take place in muscle under relaxed and stressed conditions depend on the abundance and activity of gene products of metabolic and structural pathways. In livestock at post-mortem, these muscle properties determine aspects of meat quality and are measurable. The conversion of muscle to meat mimics pathological processes associated with muscle ischemia, injury or damage in humans and it is an economic factor in pork production. Linkage, association, and expression analyses independently contributed to the identification of trait-associated molecular pathways and genes. We aim at providing multiple evidences for the role of specific genes in meat quality by integrating a genome-wide association study (GWAS) for meat quality traits and the detection of eQTL based on trait-correlated expressed genes and trait-associated markers. The GWAS revealed 51 and 200 SNPs significantly associated with meat quality in a crossbred Pietrain×(German Landrace×Large White) (Pi×(GL×LW)) and a purebred German Landrace (GL) population, respectively. Most significant SNPs in Pi×(GL×LW) were located on chromosomes (SSC) 4 and 6. The data of 47,836 eQTLs at a significance level of p<10-5 were used to scale down the number candidate genes located in these regions. These SNPs on SSC4 showed association with expression levels of ZNF704, IMPA1, and OXSR1; SSC6 SNPs were associated with expression of SIGLEC10 and PIH1D1. Most significant SNPs in GL were located on SSC6 and associated with expression levels of PIH1D1, SIGLEC10, TBCB, LOC100518735, KIF1B, LOC100514845, and two unknown genes. The abundance of transcripts of these genes in muscle, in turn, is significantly correlated with meat quality traits. We identified several genes with evidence for their candidacy for meat quality arising from the integrative approach of a genome-wide association study and eQTL analysis.
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Affiliation(s)
- Siriluck Ponsuksili
- 1. Research Group 'Functional Genome Analyses', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Eduard Murani
- 2. Research Unit 'Molecular Biology', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Nares Trakooljul
- 2. Research Unit 'Molecular Biology', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Manfred Schwerin
- 1. Research Group 'Functional Genome Analyses', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Klaus Wimmers
- 2. Research Unit 'Molecular Biology', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
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27
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Annala MJ, Parker BC, Zhang W, Nykter M. Fusion genes and their discovery using high throughput sequencing. Cancer Lett 2013; 340:192-200. [PMID: 23376639 PMCID: PMC3675181 DOI: 10.1016/j.canlet.2013.01.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/28/2012] [Accepted: 01/04/2013] [Indexed: 01/25/2023]
Abstract
Fusion genes are hybrid genes that combine parts of two or more original genes. They can form as a result of chromosomal rearrangements or abnormal transcription, and have been shown to act as drivers of malignant transformation and progression in many human cancers. The biological significance of fusion genes together with their specificity to cancer cells has made them into excellent targets for molecular therapy. Fusion genes are also used as diagnostic and prognostic markers to confirm cancer diagnosis and monitor response to molecular therapies. High-throughput sequencing has enabled the systematic discovery of fusion genes in a wide variety of cancer types. In this review, we describe the history of fusion genes in cancer and the ways in which fusion genes form and affect cellular function. We also describe computational methodologies for detecting fusion genes from high-throughput sequencing experiments, and the most common sources of error that lead to false discovery of fusion genes.
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Affiliation(s)
- M J Annala
- Tampere University of Technology, Tampere, Finland.
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28
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Hackmann K, Matko S, Gerlach EM, von der Hagen M, Klink B, Schrock E, Rump A, Di Donato N. Partial deletion of GLRB and GRIA2 in a patient with intellectual disability. Eur J Hum Genet 2012; 21:112-4. [PMID: 22669415 DOI: 10.1038/ejhg.2012.97] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report about the partial de novo loss of GLRB and GRIA2 in an individual with intellectual disability (ID). No additional mutations were found in either gene. GLRB itself does not seem to be a good candidate as it causes autosomal recessive hyperekplexia and no symptoms were found in the patient. Mutations of GRIA2 have not been described as cause of ID to date. Nonetheless, it is a very attractive candidate because it encodes a subunit of a glutamate receptor, which is highly expressed in postsynaptic structures and has an important role in signal transduction across synapses. Although we were able to isolate a fragment of a fusion transcript of both genes from the patient's blood, we were not able to isolate a transcript with an open reading frame throughout the entire length. The reading frame could be restored by differential splicing, which might take place in brain tissue but not in blood. We assume that either haploinsufficiency of GRIA2 or a GLRB/GRIA2 fusion gene leading to a protein with dominant-negative properties is causing the phenotype of the patient.
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Affiliation(s)
- Karl Hackmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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29
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Transcriptome profile in Williams–Beuren syndrome lymphoblast cells reveals gene pathways implicated in glucose intolerance and visuospatial construction deficits. Hum Genet 2010; 128:27-37. [DOI: 10.1007/s00439-010-0817-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 03/23/2010] [Indexed: 11/25/2022]
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30
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Kim BY, Cao LH, Park H, Jeong S. Reciprocal regulation of gene expression by Ephedra herba
in mouse brain. Phytother Res 2010; 24:531-7. [DOI: 10.1002/ptr.2976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Balanced translocations in mental retardation. Hum Genet 2009; 126:133-47. [PMID: 19347365 DOI: 10.1007/s00439-009-0661-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Accepted: 03/23/2009] [Indexed: 12/13/2022]
Abstract
Over the past few decades, the knowledge on genetic defects causing mental retardation has dramatically increased. In this review, we discuss the importance of balanced chromosomal translocations in the identification of genes responsible for mental retardation. We present a database-search guided overview of balanced translocations identified in patients with mental retardation. We divide those in four categories: (1) balanced translocations that helped to identify a causative gene within a contiguous gene syndrome, (2) balanced translocations that led to the identification of a mental retardation gene confirmed by independent methods, (3) balanced translocations disrupting candidate genes that have not been confirmed by independent methods and (4) balanced translocations not reported to disrupt protein coding sequences. It can safely be concluded that balanced translocations have been instrumental in the identification of multiple genes that are involved in mental retardation. In addition, many more candidate genes were identified with a suspected but (as yet?) unconfirmed role in mental retardation. Some balanced translocations do not disrupt a protein coding gene and it can be speculated that in the light of recent findings concerning ncRNA's and ultra-conserved regions, such findings are worth further investigation as these potentially may lead us to the discovery of novel disease mechanisms.
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32
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Cho JH, Jung HH, Lee SH, Im GJ, Chang J, Kim SJ. Gene expression profiles of rat olfactory bulb at developmental stage. J Neurosci Methods 2009; 177:14-9. [PMID: 18840467 DOI: 10.1016/j.jneumeth.2008.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
Abstract
Microarray analysis may be a useful tool to identify some candidate genes related to the development of olfactory bulbs. In the present study, gene expression profiles of olfactory bulbs from postnatal day 1 (P1) rats and postnatal day 35 (P35) rats were analyzed by oligonucleotide-microarray and expression levels of some selected genes were also confirmed by RT-PCR and in situ hybridization. 9146 genes were commonly identified in six microarray chips. Among these genes, 76 were up-regulated and 130 were down-regulated three-folds or more at P1 olfactory bulbs. Out of these 76 up-regulated genes, 24 genes were annotated based on the NCBI database of reference sequences and expression levels of these 24 genes were confirmed by RT-PCR. Among them, 2 interesting genes (neurogenic differentiation 1 and retinoid acid receptor alpha) were localized in the P1 olfactory bulb by the use of in situ hybridization technique. Our results may provide basic information to identify genes associated with functional growth of olfactory bulbs.
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Affiliation(s)
- Jae Hoon Cho
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Kon-Kuk University, Seoul, South Korea
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33
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Yang S, Liu T, Li S, Zhang X, Ding Q, Que H, Yan X, Wei K, Liu S. Comparative proteomic analysis of brains of naturally aging mice. Neuroscience 2008; 154:1107-20. [DOI: 10.1016/j.neuroscience.2008.04.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 04/08/2008] [Accepted: 04/09/2008] [Indexed: 11/28/2022]
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34
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Higgins AW, Alkuraya FS, Bosco AF, Brown KK, Bruns GA, Donovan DJ, Eisenman R, Fan Y, Farra CG, Ferguson HL, Gusella JF, Harris DJ, Herrick SR, Kelly C, Kim HG, Kishikawa S, Korf BR, Kulkarni S, Lally E, Leach NT, Lemyre E, Lewis J, Ligon AH, Lu W, Maas RL, MacDonald ME, Moore SD, Peters RE, Quade BJ, Quintero-Rivera F, Saadi I, Shen Y, Shendure J, Williamson RE, Morton CC. Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project. Am J Hum Genet 2008; 82:712-22. [PMID: 18319076 DOI: 10.1016/j.ajhg.2008.01.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 12/17/2007] [Accepted: 01/04/2008] [Indexed: 12/27/2022] Open
Abstract
Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.
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35
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Reiner O, Sapoznik S, Sapir T. Lissencephaly 1 linking to multiple diseases: mental retardation, neurodegeneration, schizophrenia, male sterility, and more. Neuromolecular Med 2008; 8:547-65. [PMID: 17028375 DOI: 10.1385/nmm:8:4:547] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2006] [Revised: 01/27/2006] [Accepted: 01/29/2006] [Indexed: 12/11/2022]
Abstract
Lissencephaly 1 (LIS1) was the first gene implicated in the pathogenesis of type-1 lissencephaly. More than a decade of research by multiple laboratories has revealed that LIS1 is a key node protein, which participates in several pathways, including association with the molecular motor cytoplasmic dynein, the reelin signaling pathway, and the platelet-activating factor pathway. Mutations in LIS1-interacting proteins, either in human, or in mouse models has suggested that LIS1 might play a role in the pathogenesis of numerous diseases such as male sterility, schizophrenia, neuronal degeneration, and viral infections.
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Affiliation(s)
- Orly Reiner
- Department of Molecular Genetics, The Weizmann Institute of Science, 76100 Rehovot, Israel.
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36
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Zhang G, Assadi AH, McNeil RS, Beffert U, Wynshaw-Boris A, Herz J, Clark GD, D'Arcangelo G. The Pafah1b complex interacts with the reelin receptor VLDLR. PLoS One 2007; 2:e252. [PMID: 17330141 PMCID: PMC1800349 DOI: 10.1371/journal.pone.0000252] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 01/30/2007] [Indexed: 11/18/2022] Open
Abstract
Reelin is an extracellular protein that directs the organization of cortical structures of the brain through the activation of two receptors, the very low-density lipoprotein receptor (VLDLR) and the apolipoprotein E receptor 2 (ApoER2), and the phosphorylation of Disabled-1 (Dab1). Lis1, the product of the Pafah1b1 gene, is a component of the brain platelet-activating factor acetylhydrolase 1b (Pafah1b) complex, and binds to phosphorylated Dab1 in response to Reelin. Here we investigated the involvement of the whole Pafah1b complex in Reelin signaling and cortical layer formation and found that catalytic subunits of the Pafah1b complex, Pafah1b2 and Pafah1b3, specifically bind to the NPxYL sequence of VLDLR, but not to ApoER2. Compound Pafah1b1+/−;Apoer2−/− mutant mice exhibit a reeler-like phenotype in the forebrain consisting of the inversion of cortical layers and hippocampal disorganization, whereas double Pafah1b1+/−;Vldlr−/− mutants do not. These results suggest that a cross-talk between the Pafah1b complex and Reelin occurs downstream of the VLDLR receptor.
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MESH Headings
- 1-Alkyl-2-acetylglycerophosphocholine Esterase/deficiency
- 1-Alkyl-2-acetylglycerophosphocholine Esterase/genetics
- 1-Alkyl-2-acetylglycerophosphocholine Esterase/metabolism
- Amino Acid Motifs
- Amino Acid Sequence
- Animals
- COS Cells
- Catalytic Domain
- Cell Adhesion Molecules, Neuronal/physiology
- Cell Line
- Cerebral Cortex/abnormalities
- Chlorocebus aethiops
- Extracellular Matrix Proteins/physiology
- Hippocampus/abnormalities
- Humans
- LDL-Receptor Related Proteins
- Lissencephaly/genetics
- Lissencephaly/metabolism
- Lissencephaly/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Neurologic Mutants
- Microtubule-Associated Proteins/deficiency
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Molecular Sequence Data
- Nerve Tissue Proteins/physiology
- Protein Binding
- Protein Interaction Mapping
- Receptors, Cell Surface/deficiency
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Receptors, LDL/deficiency
- Receptors, LDL/genetics
- Receptors, LDL/metabolism
- Receptors, LDL/physiology
- Receptors, Lipoprotein/deficiency
- Receptors, Lipoprotein/genetics
- Receptors, Lipoprotein/metabolism
- Receptors, Lipoprotein/physiology
- Recombinant Fusion Proteins/metabolism
- Reelin Protein
- Serine Endopeptidases/physiology
- Signal Transduction/physiology
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Affiliation(s)
- Guangcheng Zhang
- The Cain Foundation Laboratories, Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Amir H. Assadi
- The Cain Foundation Laboratories, Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Robert S. McNeil
- The Cain Foundation Laboratories, Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Uwe Beffert
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Anthony Wynshaw-Boris
- Department of Pediatrics and Medicine, University of California, San Diego School of Medicine, La Jolla, California, United States of America
| | - Joachim Herz
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Gary D. Clark
- The Cain Foundation Laboratories, Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neurology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gabriella D'Arcangelo
- The Cain Foundation Laboratories, Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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Cha MH, Rhim T, Kim KH, Jang AS, Paik YK, Park CS. Proteomic identification of macrophage migration-inhibitory factor upon exposure to TiO2 particles. Mol Cell Proteomics 2006; 6:56-63. [PMID: 17028300 DOI: 10.1074/mcp.m600234-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Inhalation of particulate matter aggravates respiratory symptoms in patients with chronic airway diseases, but the mechanisms underlying this response remain poorly understood. We used a proteomics approach to examine this phenomenon. Treatment of epithelial cells with BSA-coated titanium dioxide (TiO(2)) particles altered 20 protein spots on the two-dimensional gel, and these were then analyzed by nano-LC-MS/MS. These proteins included defense-related, cell-activating, and cytoskeletal proteins implicated in the response to oxidative stress. The proteins were classified into four groups according to the time course of their expression patterns. For validation, RT-PCR was performed on extracts of in vitro TiO(2)-treated cells, and lung issues from TiO(2)-treated rats were analyzed by immunohistochemical staining and enzyme immunoassay. TiO(2) treatment was found to increase the amount of mRNA for macrophage migration-inhibitory factor (MIF). MIF was expressed primarily in epithelium and was elevated in lung tissues and bronchoalveolar lavage fluids of TiO(2)-treated rats as compared with sham-treated rats. Carbon black and diesel exhaust particles also induced expression of MIF protein in the epithelial cells.
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Affiliation(s)
- Myung-Hwa Cha
- Genome Research Center for Allergy and Respiratory Diseases, Soonchunhyang University Hospital, Bucheon-si, Gyeonggi-do 420-853, Korea
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D'Arcangelo G. Reelin mouse mutants as models of cortical development disorders. Epilepsy Behav 2006; 8:81-90. [PMID: 16266828 DOI: 10.1016/j.yebeh.2005.09.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Revised: 09/09/2005] [Accepted: 09/10/2005] [Indexed: 11/23/2022]
Abstract
Developmental defects in neuronal positioning and synaptic connectivity are commonly found in neurological diseases, and they are believed to underlie many cognitive and affective disorders. Several mouse mutants are currently available that model at least some aspects of human developmental brain disorders. With the identification of the genes mutated in these animals and the study of the cellular basis of the phenotypes, we have taken significant strides toward an understanding of the mechanisms controlling proper brain development and the consequences of their dysfunction. In particular, mouse mutants deficient in the Reelin gene have provided valuable insights into the mechanisms of cortical development. Absence of Reelin expression in the spontaneous mutant mouse reeler leads to extensive defects in neuronal position and dendrite development. In humans, loss of Reelin results in a type of lissencephaly with severe cortical and cerebellar malformation. Genetic and biochemical studies using mouse mutants suggest that the Lis1 protein may participate in the Reelin signaling pathway controlling cortical development. Reduced levels of Reelin are also present in postmortem brains of patients with schizophrenia, suggesting a possible link with this cognitive disorder. The regulation of the Reelin gene may thus provide insights into the mechanisms of this disease.
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Affiliation(s)
- Gabriella D'Arcangelo
- The Cain Foundation Laboratories, Texas Children's Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
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Abstract
Genetic factors have an important role in the aetiology of mental retardation. However, their contribution is often underestimated because in developed countries, severely affected patients are mainly sporadic cases and familial cases are rare. X-chromosomal mental retardation is the exception to this rule, and this is one of the reasons why research into the genetic and molecular causes of mental retardation has focused almost entirely on the X-chromosome. Here, we review the remarkable recent progress in this field, its promise for understanding neural function, learning and memory, and the implications of this research for health care.
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Affiliation(s)
- H-Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
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Sutajová M, Neukirchen U, Meinecke P, Czeizel AE, Tímár L, Sólyom E, Gal A, Kutsche K. Disruption of the PDGFB gene in a 1;22 translocation patient does not cause Costello syndrome. Genomics 2004; 83:883-92. [PMID: 15081117 DOI: 10.1016/j.ygeno.2003.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Accepted: 10/30/2003] [Indexed: 10/26/2022]
Abstract
We studied a female patient initially diagnosed with Costello syndrome who carries an apparently balanced translocation, t(1;22) (q24.3;q13.1). Molecular characterization of the translocation revealed a mosaic of two derivative chromosomes 1 in her peripheral blood lymphocytes, in one of which the coding region of the platelet-derived growth factor (PDGFB; chromosome 22q13.1) gene was disrupted. Both the initial translocation and the secondary intrachromosomal rearrangement appear to have occurred by nonhomologous (illegitimate) recombination. In 18 patients with Costello syndrome, mutation analysis of the genes belonging to the PDGF/R family, PDGFA, PDGFB, PDGFC, PDGFD, PDGFRA, and PDGFRB, revealed no pathogenic mutations. Reevaluation of the clinical symptoms of the translocation patient challenges the diagnosis of Costello syndrome in this patient. In total RNA isolated from lymphocytes of the translocation patient, we identified four different fusion transcripts consisting of PDGFB exons and parts of chromosome 1q24.3. In two of the mRNAs, exon 6 of PDGFB, encoding the 41 C-terminal amino acid residues, was absent. Immunofluorescence analysis showed that the wild-type protein was dispersed and formed a network-like structure in the extracellular matrix, whereas the two aberrant PDGFB proteins were localized in aggregates. We speculate that the biological consequences of the mutant PDGFB allele contributed to the unique disease phenotype of the translocation patient.
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MESH Headings
- Abnormalities, Multiple/genetics
- Animals
- COS Cells
- Child
- Chromosome Breakage/genetics
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 22/genetics
- DNA Mutational Analysis
- Exons/genetics
- Extracellular Matrix/metabolism
- Female
- Genes, sis/genetics
- Humans
- Male
- Phenotype
- Platelet-Derived Growth Factor/chemistry
- Platelet-Derived Growth Factor/genetics
- Platelet-Derived Growth Factor/metabolism
- Polymorphism, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Syndrome
- Translocation, Genetic/genetics
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Affiliation(s)
- Markéta Sutajová
- Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Butenfeld 42, 22529 Hamburg, Germany
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Koizumi H, Yamaguchi N, Hattori M, Ishikawa TO, Aoki J, Taketo MM, Inoue K, Arai H. Targeted disruption of intracellular type I platelet activating factor-acetylhydrolase catalytic subunits causes severe impairment in spermatogenesis. J Biol Chem 2003; 278:12489-94. [PMID: 12551946 DOI: 10.1074/jbc.m211836200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intracellular type I platelet activating factor-acetylhydrolase is a phospholipase that consists of a dimer of two homologous catalytic subunits alpha1 and alpha2 as well as LIS1, a product of the causative gene for type I lissencephaly. LIS1 plays an important role in neuronal migration during brain development, but the in vivo function of the catalytic subunits remains unclear. In this study, we generated alpha1- and a2-deficient mice by targeted disruption. alpha1(-/-) mice are indistinguishable from wild-type mice, whereas alpha2(-/-) male mice show a significant reduction in testis size. Double-mutant male mice are sterile because of severe impairment of spermatogenesis. Histological examination revealed marked degeneration at the spermatocyte stage and an increase of apoptotic cells in the seminiferous tubules. The catalytic subunits are expressed at high levels in testis as well as brain in mice. In wild-type mice, alpha2 is expressed in all seminiferous tubule cell types, whereas alpha1 is expressed only in the spermatogonia. This expression pattern parallels the finding that deletion of both subunits induces a marked loss of germ cells at an early spermatogenic stage. We also found that the LIS1 protein levels, but not the mRNA levels, were significantly reduced in alpha2(-/-) and double-mutant mice, suggesting that the catalytic subunits, especially alpha2, are a determinant of LIS1 expression level.
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Affiliation(s)
- Hiroyuki Koizumi
- Department of Health Chemistry and Laboratory of Biomedical Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
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Abstract
Platelet-activating factor (PAF) is one of the most potent lipid mediators and is involved in a variety of physiological events. The acetyl group at the sn-2 position of its glycerol backbone is required for its biological activity, and deacetylation of PAF induces loss of activity. The deacetylation reaction is catalyzed by PAF-acetylhydrolase (PAF-AH). A series of biochemical and enzymological studies have revealed that there are at least three types of PAF-AH in mammals, namely the intracellular type I and II and plasma type. Type I PAF-AH is a G-protein-like complex of two catalytic subunits (alpha1 and alpha2) and a regulatory beta subunit. The beta subunit is a product of the LIS1 gene, mutations of which cause type I lissencephaly. Recent studies indicate that LIS1/beta is important in cellular functions such as induction of nuclear movement and control of microtubule organization. Although circumstantial evidence is accumulating supporting the idea that the catalytic subunits are also involved in microtubule function, it is still not known what role PAF plays in the process and whether PAF is a native endogenous substrate of this enzyme. Type II PAF-AH is a single polypeptide and shows significant sequence homology with plasma PAF-AH. Type II PAF-AH is myristoylated at the N-terminus and like other N-myristoylated proteins, is distributed in both the cytosol and membranes. Plasma PAF-AH is also a single polypeptide and exists in association with plasma lipoproteins. Type II PAF-AH as well as plasma PAF-AH may play roles as scavengers of oxidized phospholipids which are thought to be involved in diverse pathological processes, including disorganization of membrane structure and PAF-like proinflammatory actions. In this chapter, author focuses on the structures and possible biological functions of intracellular PAF-AHs.
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Affiliation(s)
- Hiroyuki Arai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Japan.
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