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Ryu SW, Yoon J, Kim D, Han B, Han H, Han J, Lee H, Seo GH, Lee BH. Identification of a complex intrachromosomal inverted insertion in the long arm of chromosome 9 as a cause of tuberous sclerosis complex in a Korean family. Mol Genet Genomic Med 2024; 12:e2330. [PMID: 38265426 PMCID: PMC10958175 DOI: 10.1002/mgg3.2330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem disorder, caused by a loss-of-function of either TSC1 or TSC2 gene. However, in 10%-15% TSC patients there is no pathogenic variant identified in either TSC1 or TSC2 genes based on standard clinical testing. METHODS In this study, genome sequencing was performed for families with clinical diagnosis of TSC with negative results from TSC1 and TSC2 single-gene tests. RESULTS Herein, we report a family presenting a classical TSC phenotype with an unusual, complex structural variant involving the TSC1 gene: an intrachromosomal inverted insertion in the long arm of chromosome 9. We speculate that the inverted 9q33.3q34.13 region was inserted into the q31.2 region with the 3'-end of the breakpoint of the inversion being located within the TSC1 gene, resulting in premature termination of TSC1. CONCLUSIONS In this study, we demonstrate the utility of genome sequencing for the identification of complex chromosomal rearrangement. Because the breakpoints are located within the deep intronic/intergenic region, this copy-neutral variant was missed by the TSC1 and TSC2 single-gene tests and contributed to an unknown etiology. Together, this finding suggests that complex structural variants may be underestimated causes for the etiology of TSC.
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Affiliation(s)
| | - Ji‐Hee Yoon
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | | | | | | | | | | | | | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
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2
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Primiani CT, Lee JK, O’Brien CE, Chen MW, Perin J, Kulikowicz E, Santos P, Adams S, Lester B, Rivera-Diaz N, Olberding V, Niedzwiecki MV, Ritzl EK, Habela CW, Liu X, Yang ZJ, Koehler RC, Martin LJ. Hypothermic Protection in Neocortex Is Topographic and Laminar, Seizure Unmitigating, and Partially Rescues Neurons Depleted of RNA Splicing Protein Rbfox3/NeuN in Neonatal Hypoxic-Ischemic Male Piglets. Cells 2023; 12:2454. [PMID: 37887298 PMCID: PMC10605428 DOI: 10.3390/cells12202454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
The effects of hypothermia on neonatal encephalopathy may vary topographically and cytopathologically in the neocortex with manifestations potentially influenced by seizures that alter the severity, distribution, and type of neuropathology. We developed a neonatal piglet survival model of hypoxic-ischemic (HI) encephalopathy and hypothermia (HT) with continuous electroencephalography (cEEG) for seizures. Neonatal male piglets received HI-normothermia (NT), HI-HT, sham-NT, or sham-HT treatments. Randomized unmedicated sham and HI piglets underwent cEEG during recovery. Survival was 2-7 days. Normal and pathological neurons were counted in different neocortical areas, identified by cytoarchitecture and connectomics, using hematoxylin and eosin staining and immunohistochemistry for RNA-binding FOX-1 homolog 3 (Rbfox3/NeuN). Seizure burden was determined. HI-NT piglets had a reduced normal/total neuron ratio and increased ischemic-necrotic/total neuron ratio relative to sham-NT and sham-HT piglets with differing severities in the anterior and posterior motor, somatosensory, and frontal cortices. Neocortical neuropathology was attenuated by HT. HT protection was prominent in layer III of the inferior parietal cortex. Rbfox3 immunoreactivity distinguished cortical neurons as: Rbfox3-positive/normal, Rbfox3-positive/ischemic-necrotic, and Rbfox3-depleted. HI piglets had an increased Rbfox3-depleted/total neuron ratio in layers II and III compared to sham-NT piglets. Neuronal Rbfox3 depletion was partly rescued by HT. Seizure burdens in HI-NT and HI-HT piglets were similar. We conclude that the neonatal HI piglet neocortex has: (1) suprasylvian vulnerability to HI and seizures; (2) a limited neuronal cytopathological repertoire in functionally different regions that engages protective mechanisms with HT; (3) higher seizure burden, insensitive to HT, that is correlated with more panlaminar ischemic-necrotic neurons in the somatosensory cortex; and (4) pathological RNA splicing protein nuclear depletion that is sensitive to HT. This work demonstrates that HT protection of the neocortex in neonatal HI is topographic and laminar, seizure unmitigating, and restores neuronal depletion of RNA splicing factor.
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Affiliation(s)
- Christopher T. Primiani
- Department of Neurology, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
| | - Jennifer K. Lee
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Caitlin E. O’Brien
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - May W. Chen
- Department Pediatrics, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
| | - Jamie Perin
- Department of Biostatistics and Epidemiology, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
| | - Ewa Kulikowicz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Polan Santos
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Shawn Adams
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Bailey Lester
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Natalia Rivera-Diaz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Valerie Olberding
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Mark V. Niedzwiecki
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Eva K. Ritzl
- Department of Neurology, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
| | - Christa W. Habela
- Department of Neurology, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
| | - Xiuyun Liu
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Zeng-Jin Yang
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Raymond C. Koehler
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
| | - Lee J. Martin
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA; (J.K.L.); (E.K.); (V.O.); (M.V.N.)
- Department of Pathology, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
- The Pathobiology Graduate Training Program, Johns Hopkins University School of Medicine, 558 Ross Building, 720 Rutland Avenue, Baltimore, MD 21205-2196, USA
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Sahajpal NS, Jeffrey DHF, DuPont BR, Hilton B. 17q25.3 copy number changes: association with neurodevelopmental disorders and cardiac malformation. Mol Cytogenet 2023; 16:15. [PMID: 37430334 DOI: 10.1186/s13039-023-00644-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/19/2023] [Indexed: 07/12/2023] Open
Abstract
Copy number variants (CNVs) have been identified as common genomic variants that play a significant role in inter-individual variability. Conversely, rare recurrent CNVs have been found to be causal for many disorders with well-established genotype-phenotype relationships. However, the phenotypic implications of rare non-recurrent CNVs remain poorly understood. Herein, we re-investigated 18,542 cases reported from chromosomal microarray at Greenwood Genetic Center from 2010 to 2022 and identified 15 cases with CNVs involving the 17q25.3 region. We report the detailed clinical features of these subjects, and compare with the cases reported in the literature to determine genotype-phenotype correlations for a subset of genes in this region. The CNVs in the 17q25.3 region were found to be rare events, with a prevalence of 0.08% (15/18542) observed in our cohort. The CNVs were dispersed across the entire 17q25.3 region with variable breakpoints and no smallest region of overlap. The subjects presented with a wide range of clinical features, with neurodevelopmental disorders (autism spectrum disorder, intellectual disability, developmental delay) being the most common features (80%), then expressive language disorder (33%), and finally cardiovascular malformations (26%). The association of CNVs involving the critical gene-rich region of 17q25.3 with neurodevelopmental disorders and cardiac malformation, implicates several genes as plausible drivers for these events.
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Affiliation(s)
| | - David H F Jeffrey
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Barbara R DuPont
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Benjamin Hilton
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, SC, 29646, USA.
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4
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Zeng X, Lin D, Liang D, Huang J, Yi J, Lin D, Zhang Z. Gene sequencing and result analysis of balanced translocation carriers by third-generation gene sequencing technology. Sci Rep 2023; 13:7004. [PMID: 37117255 PMCID: PMC10147651 DOI: 10.1038/s41598-022-20356-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/12/2022] [Indexed: 04/30/2023] Open
Abstract
Because the total gene copy number remains constant and all genes are normally expressed, carriers of balanced chromosomal translocations usually have a normal phenotype but are able to produce many different types of gametes during meiosis, and unbalanced gametes lead to increased risks of infertility, recurrent spontaneous abortion, stillbirth, neonatal death or malformations and intellectual abnormalities in offspring. The key to balanced translocations lies in finding the breakpoints, but current genetic testing techniques are all short-read sequencing, with the disadvantage of procedural complexity and imprecision for precisely identifying the breakpoints. The latest third-generation sequencing technology overcomes these drawbacks and uses robust long-read sequencing to accurately and rapidly detect genome-wide information and identify breakpoint locations. In this paper, we performed whole genome long-read sequencing using an Oxford Nanopore sequencer to detect the breakpoints of 4 balanced chromosomal translocation carriers. The results showed that employing about ~ 10× coverage confirmed 6 of the 8 breakpoints, of which, 2 had microdeletions/insertions identified near the breakpoints and 4 had breakpoints that disrupted the normal gene structure and were simultaneously tested for genome-wide structural variation (SV). The results show that whole genome long-read sequencing is an efficient method for pinpointing translocation breakpoints and providing genome-wide information, which is essential for medical genetics and preimplantation genetic testing.
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Affiliation(s)
- Xiaoqi Zeng
- Fujian Provincial Sperm Bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.
- Obstetrics Department of Longyan First Hospital of Fujian Medical University, Fuzhou, China.
| | - Dandan Lin
- Fujian Provincial Sperm Bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Danhong Liang
- Fujian Provincial Sperm Bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Jingwen Huang
- Fujian Provincial Sperm Bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Jinsong Yi
- Fujian Provincial Sperm Bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Dianliang Lin
- Fujian Provincial Sperm Bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.
| | - Zhengmian Zhang
- Fujian Provincial Sperm Bank, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
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5
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Soo CC, Brandenburg JT, Nebel A, Tollman S, Berkman L, Ramsay M, Choudhury A. Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community. Commun Biol 2023; 6:328. [PMID: 36973338 PMCID: PMC10043003 DOI: 10.1038/s42003-023-04636-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
Cognitive function is an indicator for global physical and mental health, and cognitive impairment has been associated with poorer life outcomes and earlier mortality. A standard cognition test, adapted to a rural-dwelling African community, and the Oxford Cognition Screen-Plus were used to capture cognitive performance as five continuous traits (total cognition score, verbal episodic memory, executive function, language, and visuospatial ability) for 2,246 adults in this population of South Africans. A novel common variant, rs73485231, reached genome-wide significance for association with episodic memory using data for ~14 million markers imputed from the H3Africa genotyping array data. Window-based replication of previously implicated variants and regions of interest support the discovery of African-specific associated variants despite the small population size and low allele frequency. This African genome-wide association study identifies suggestive associations with general cognition and domain-specific cognitive pathways and lays the groundwork for further genomic studies on cognition in Africa.
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Affiliation(s)
- Cassandra C Soo
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Almut Nebel
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lisa Berkman
- MRC/Wits Rural Public Health and Health Transitions Research Unit, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Center for Population and Development Studies, Harvard University, Cambridge, MA, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Abstract
Human chromosome inversions are types of balanced structural variations, making them difficult to analyze. Thanks to PEM (paired-end sequencing and mapping), there has been tremendous progress in studying inversions. Inversions play an important role as an evolutionary factor, contributing to the formation of gonosomes, speciation of chimpanzees and humans, and inv17q21.3 or inv8p23.1 exhibit the features of natural selection. Both inversions have been related to pathogenic phenotype by directly affecting a gene structure (e.g., inv5p15.1q14.1), regulating gene expression (e.g., inv7q21.3q35) and by predisposing to other secondary arrangements (e.g., inv7q11.23). A polymorphism of human inversions is documented by the InvFEST database (a database that stores information about clinical predictions, validations, frequency of inversions, etc.), but only a small fraction of these inversions is validated, and a detailed analysis is complicated by the frequent location of breakpoints within regions of repetitive sequences.
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Affiliation(s)
- Klara Kosuthova
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roman Solc
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
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Aristidou C, Theodosiou A, Alexandrou A, Papaevripidou I, Evangelidou P, Kosmaidou-Aravidou Z, Behjati F, Christophidou-Anastasiadou V, Tanteles GA, Sismani C. Exploring the Genetic Causality of Discordant Phenotypes in Familial Apparently Balanced Translocation Cases Using Whole Exome Sequencing. Genes (Basel) 2022; 14. [PMID: 36672823 DOI: 10.3390/genes14010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Familial apparently balanced translocations (ABTs) are usually not associated with a phenotype; however, rarely, ABTs segregate with discordant phenotypes in family members carrying identical rearrangements. The current study was a follow-up investigation of four familial ABTs, where whole exome sequencing (WES) was implemented as a diagnostic tool to identify the underlying genetic aetiology of the patients' phenotypes. Data were analysed using an in-house bioinformatics pipeline alongside VarSome Clinical. WES findings were validated with Sanger sequencing, while the impact of splicing and missense variants was assessed by reverse-transcription PCR and in silico tools, respectively. Novel candidate variants were identified in three families. In family 1, it was shown that the de novo pathogenic STXBP1 variant (NM_003165.6:c.1110+2T>G) affected splicing and segregated with the patient's phenotype. In family 2, a likely pathogenic TUBA1A variant (NM_006009.4:c.875C>T, NP_006000.2:p.(Thr292Ile)) could explain the patient's symptoms. In family 3, an SCN1A variant of uncertain significance (NM_006920.6:c.5060A>G, NP_008851.3:p.(Glu1687Gly)) required additional evidence to sufficiently support causality. This first report of WES application in familial ABT carriers with discordant phenotypes supported our previous findings describing such rearrangements as coincidental. Thus, WES can be recommended as a complementary test to find the monogenic cause of aberrant phenotypes in familial ABT carriers.
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Munoz-Ballester C, Mahmutovic D, Rafiqzad Y, Korot A, Robel S. Mild Traumatic Brain Injury-Induced Disruption of the Blood-Brain Barrier Triggers an Atypical Neuronal Response. Front Cell Neurosci 2022; 16:821885. [PMID: 35250487 PMCID: PMC8894613 DOI: 10.3389/fncel.2022.821885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/17/2022] [Indexed: 12/03/2022] Open
Abstract
Mild TBI (mTBI), which affects 75% of TBI survivors or more than 50 million people worldwide each year, can lead to consequences including sleep disturbances, cognitive impairment, mood swings, and post-traumatic epilepsy in a subset of patients. To interrupt the progression of these comorbidities, identifying early pathological events is key. Recent studies have shown that microbleeds, caused by mechanical impact, persist for months after mTBI and are correlated to worse mTBI outcomes. However, the impact of mTBI-induced blood-brain barrier damage on neurons is yet to be revealed. We used a well-characterized mouse model of mTBI that presents with frequent and widespread but size-restricted damage to the blood-brain barrier to assess how neurons respond to exposure of blood-borne factors in this pathological context. We used immunohistochemistry and histology to assess the expression of neuronal proteins in excitatory and inhibitory neurons after mTBI. We observed that the expression of NeuN, Parvalbumin, and CamKII was lost within minutes in areas with blood-brain barrier disruption. Yet, the neurons remained alive and could be detected using a fluorescent Nissl staining even 6 months later. A similar phenotype was observed after exposure of neurons to blood-borne factors due to endothelial cell ablation in the absence of a mechanical impact, suggesting that entrance of blood-borne factors into the brain is sufficient to induce the neuronal atypical response. Changes in postsynaptic spines were observed indicative of functional changes. Thus, this study demonstrates That exposure of neurons to blood-borne factors causes a rapid and sustained loss of neuronal proteins and changes in spine morphology in the absence of neurodegeneration, a finding that is likely relevant to many neuropathologies.
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Affiliation(s)
- Carmen Munoz-Ballester
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Dzenis Mahmutovic
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yusuf Rafiqzad
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- School of Neuroscience, Virginia Tech Carilion, Blacksburg, VA, United States
| | - Alia Korot
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Kenyon College, Gambier, OH, United States
| | - Stefanie Robel
- Fralin Biomedical Research Institute, Virginia Tech Carilion, Roanoke, VA, United States
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
- School of Neuroscience, Virginia Tech Carilion, Blacksburg, VA, United States
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Huang M, Lou D, Charli A, Kong D, Jin H, Zenitsky G, Anantharam V, Kanthasamy A, Wang Z, Kanthasamy AG. Mitochondrial dysfunction-induced H3K27 hyperacetylation perturbs enhancers in Parkinson's disease. JCI Insight 2021; 6:e138088. [PMID: 34494552 PMCID: PMC8492320 DOI: 10.1172/jci.insight.138088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dysfunction is a major pathophysiological contributor to the progression of Parkinson’s disease (PD); however, whether it contributes to epigenetic dysregulation remains unknown. Here, we show that both chemically and genetically driven mitochondrial dysfunctions share a common mechanism of epigenetic dysregulation. Under both scenarios, lysine 27 acetylation of likely variant H3.3 (H3.3K27ac) increased in dopaminergic neuronal models of PD, thereby opening that region to active enhancer activity via H3K27ac. These vulnerable epigenomic loci represent potential transcription factor motifs for PD pathogenesis. We further confirmed that mitochondrial dysfunction induces H3K27ac in ex vivo and in vivo (MitoPark) neurodegenerative models of PD. Notably, the significantly increased H3K27ac in postmortem PD brains highlights the clinical relevance to the human PD population. Our results reveal an exciting mitochondrial dysfunction-metabolism-H3K27ac-transcriptome axis for PD pathogenesis. Collectively, the mechanistic insights link mitochondrial dysfunction to epigenetic dysregulation in dopaminergic degeneration and offer potential new epigenetic intervention strategies for PD.
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Affiliation(s)
- Minhong Huang
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Dan Lou
- Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Adhithiya Charli
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Dehui Kong
- Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei Province, China
| | - Huajun Jin
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Gary Zenitsky
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Vellareddy Anantharam
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Arthi Kanthasamy
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Zhibin Wang
- Laboratory of Environmental Epigenomes, Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei Province, China
| | - Anumantha G Kanthasamy
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
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Li R, Wang J, Gu A, Xu Y, Guo J, Pan J, Zeng Y, Ma Y, Zhou C, Xu Y. Feasibility study of using unbalanced embryos as a reference to distinguish euploid carrier from noncarrier embryos by single nucleotide polymorphism array for reciprocal translocations. Prenat Diagn 2021; 41:681-689. [PMID: 33411373 DOI: 10.1002/pd.5897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVES To study the feasibility of using unbalanced embryos as a reference in distinguishing euploid carrier and noncarrier embryos by single nucleotide polymorphism (SNP) array-based preimplantation genetic testing (PGT) for reciprocal translocations. METHODS After comprehensive chromosome screening (CCS), euploid embryos were identified as normal or carriers using a family member as a reference. Next, unbalanced embryos were used as a reference, and the results were compared with the previous ones. Karyotypes of transferred embryos were validated by prenatal diagnosis. RESULTS Of 995 embryos from 110 couples, 288 were found to be euploid. Using a family member as a reference, 142 and 144 embryos were tested to be euploid noncarrier and carrier respectively, and the remaining 2 embryos were undetermined. When unbalanced embryos were selected as references, all the results were consistent with the previous ones. A total of 107 embryos were transferred, resulting in 66 clinical pregnancies. Karyotypes of prenatal diagnosis were all in accordance with the results of tested embryos. CONCLUSIONS SNP array-based haplotyping is a rapid and effective way to distinguish between euploid carrier and noncarrier embryos. In case no family member is available as a reference, unbalanced embryos can be used for identification of euploid carrier and noncarrier embryos.
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Affiliation(s)
- Rong Li
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Jing Wang
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Ailing Gu
- Department of Cardiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yan Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Jing Guo
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Jiafu Pan
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Yanhong Zeng
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Yuanlin Ma
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Canquan Zhou
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
| | - Yanwen Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, Guangdong, China
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11
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Barthélémy I, Calmels N, Weiss RB, Tiret L, Vulin A, Wein N, Peccate C, Drougard C, Beroud C, Deburgrave N, Thibaud JL, Escriou C, Punzón I, Garcia L, Kaplan JC, Flanigan KM, Leturcq F, Blot S. X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation. Skelet Muscle 2020; 10:23. [PMID: 32767978 PMCID: PMC7412789 DOI: 10.1186/s13395-020-00239-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/09/2020] [Indexed: 12/24/2022] Open
Abstract
Background Canine models of Duchenne muscular dystrophy (DMD) are a valuable tool to evaluate potential therapies because they faithfully reproduce the human disease. Several cases of dystrophinopathies have been described in canines, but the Golden Retriever muscular dystrophy (GRMD) model remains the most used in preclinical studies. Here, we report a new spontaneous dystrophinopathy in a Labrador Retriever strain, named Labrador Retriever muscular dystrophy (LRMD). Methods A colony of LRMD dogs was established from spontaneous cases. Fourteen LRMD dogs were followed-up and compared to the GRMD standard using several functional tests. The disease causing mutation was studied by several molecular techniques and identified using RNA-sequencing. Results The main clinical features of the GRMD disease were found in LRMD dogs; the functional tests provided data roughly overlapping with those measured in GRMD dogs, with similar inter-individual heterogeneity. The LRMD causal mutation was shown to be a 2.2-Mb inversion disrupting the DMD gene within intron 20 and involving the TMEM47 gene. In skeletal muscle, the Dp71 isoform was ectopically expressed, probably as a consequence of the mutation. We found no evidence of polymorphism in either of the two described modifier genes LTBP4 and Jagged1. No differences were found in Pitpna mRNA expression levels that would explain the inter-individual variability. Conclusions This study provides a full comparative description of a new spontaneous canine model of dystrophinopathy, found to be phenotypically equivalent to the GRMD model. We report a novel large DNA mutation within the DMD gene and provide evidence that LRMD is a relevant model to pinpoint additional DMD modifier genes.
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Affiliation(s)
- Inès Barthélémy
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Nadège Calmels
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France.,Laboratoire de Diagnostic Génétique-Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, 1 Place de L'Hôpital, 67091, Strasbourg, France
| | - Robert B Weiss
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Laurent Tiret
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Adeline Vulin
- SQY Therapeutics, Université de Versailles Saint-Quentin-en-Yvelines, Montigny le Bretonneux, France
| | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Cécile Peccate
- SQY Therapeutics, Université de Versailles Saint-Quentin-en-Yvelines, Montigny le Bretonneux, France.,Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, Centre de Recherche en Myologie, Institut de Myologie, G.H. Pitié Salpêtrière, Paris, France
| | - Carole Drougard
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Christophe Beroud
- Aix Marseille Université, INSERM, MMG, Bioinformatics & Genetics, Marseille, France.,APHM, Hôpital Timone Enfants, Laboratoire de Génétique Moléculaire, Marseille, France
| | - Nathalie Deburgrave
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Jean-Laurent Thibaud
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Catherine Escriou
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Isabel Punzón
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Luis Garcia
- Université de Versailles Saint-Quentin-en-Yvelines, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France
| | - Jean-Claude Kaplan
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Kevin M Flanigan
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - France Leturcq
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, Centre de Recherche en Myologie, Institut de Myologie, G.H. Pitié Salpêtrière, Paris, France
| | - Stéphane Blot
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France.
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12
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Kaya M, Bağatır Ozan G, Çefle K, Öztürk Ş, Palanduz Ş. De novo t(1;6)(p13p21.3) Dengeli Resiprokal Translokasyonun İnfertilite ile İlişkisi. Düzce Üniversitesi Sağlık Bilimleri Enstitüsü Dergisi 2020. [DOI: 10.33631/duzcesbed.556258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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Hu L, Liang F, Cheng D, Zhang Z, Yu G, Zha J, Wang Y, Xia Q, Yuan D, Tan Y, Wang D, Liang Y, Lin G. Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform. Front Genet 2020; 10:1313. [PMID: 32010185 PMCID: PMC6972507 DOI: 10.3389/fgene.2019.01313] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/29/2019] [Indexed: 02/02/2023] Open
Abstract
Genomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular, balanced translocations and inversions can neither be identified by microarrays since they do not alter chromosome copy numbers, nor by short-read sequencing because of the unmappability of short reads against repetitive genomic regions. The precise localization of breakpoints is vital for exploring genetic causes in patients with balanced translocations or inversions. Long-read sequencing techniques may detect these structural variants in a more direct, efficient, and accurate manner. Here, we performed whole-genome, long-read sequencing using the Oxford Nanopore GridION sequencer to detect breakpoints in six balanced chromosome translocation carriers and one inversion carrier. The results showed that all the breakpoints were consistent with the karyotype results with only ~10× coverage. Polymerase chain reaction (PCR) and Sanger sequencing confirmed 8 out of 14 breakpoints; however, other breakpoint loci were slightly missed since they were either in highly repetitive regions or pericentromeric regions. Some of the breakpoints interrupted normal gene structure, and in other cases, micro-deletions/insertions were found just next to the breakpoints. We also detected haplotypes around the breakpoint regions. Our results suggest that long-read, whole-genome sequencing is an ideal strategy for precisely localizing translocation breakpoints and providing haplotype information, which is essential for medical genetics and preimplantation genetic testing.
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Affiliation(s)
- Liang Hu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,Key Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, China.,Department of Research, National Engineering Research Center of Human Stem Cells, Changsha, China
| | - Fan Liang
- GrandOmics Biosciences, Beijing, China
| | - Dehua Cheng
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Research, National Engineering Research Center of Human Stem Cells, Changsha, China
| | | | | | | | - Yang Wang
- GrandOmics Biosciences, Beijing, China
| | - Qi Xia
- GrandOmics Biosciences, Beijing, China
| | | | - Yueqiu Tan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,Key Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, China.,Department of Research, National Engineering Research Center of Human Stem Cells, Changsha, China
| | | | - Yu Liang
- GrandOmics Biosciences, Beijing, China
| | - Ge Lin
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Department of Genetics, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,Key Laboratory of Reproductive and Stem Cell Engineering, National Health and Family Planning Commission, Changsha, China.,Department of Research, National Engineering Research Center of Human Stem Cells, Changsha, China
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14
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Schluth-Bolard C, Diguet F, Chatron N, Rollat-Farnier PA, Bardel C, Afenjar A, Amblard F, Amiel J, Blesson S, Callier P, Capri Y, Collignon P, Cordier MP, Coubes C, Demeer B, Chaussenot A, Demurger F, Devillard F, Doco-Fenzy M, Dupont C, Dupont JM, Dupuis-Girod S, Faivre L, Gilbert-Dussardier B, Guerrot AM, Houlier M, Isidor B, Jaillard S, Joly-Hélas G, Kremer V, Lacombe D, Le Caignec C, Lebbar A, Lebrun M, Lesca G, Lespinasse J, Levy J, Malan V, Mathieu-Dramard M, Masson J, Masurel-Paulet A, Mignot C, Missirian C, Morice-Picard F, Moutton S, Nadeau G, Pebrel-Richard C, Odent S, Paquis-Flucklinger V, Pasquier L, Philip N, Plutino M, Pons L, Portnoï MF, Prieur F, Puechberty J, Putoux A, Rio M, Rooryck-Thambo C, Rossi M, Sarret C, Satre V, Siffroi JP, Till M, Touraine R, Toutain A, Toutain J, Valence S, Verloes A, Whalen S, Edery P, Tabet AC, Sanlaville D. Whole genome paired-end sequencing elucidates functional and phenotypic consequences of balanced chromosomal rearrangement in patients with developmental disorders. J Med Genet 2019; 56:526-535. [PMID: 30923172 DOI: 10.1136/jmedgenet-2018-105778] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/30/2019] [Accepted: 02/20/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Balanced chromosomal rearrangements associated with abnormal phenotype are rare events, but may be challenging for genetic counselling, since molecular characterisation of breakpoints is not performed routinely. We used next-generation sequencing to characterise breakpoints of balanced chromosomal rearrangements at the molecular level in patients with intellectual disability and/or congenital anomalies. METHODS Breakpoints were characterised by a paired-end low depth whole genome sequencing (WGS) strategy and validated by Sanger sequencing. Expression study of disrupted and neighbouring genes was performed by RT-qPCR from blood or lymphoblastoid cell line RNA. RESULTS Among the 55 patients included (41 reciprocal translocations, 4 inversions, 2 insertions and 8 complex chromosomal rearrangements), we were able to detect 89% of chromosomal rearrangements (49/55). Molecular signatures at the breakpoints suggested that DNA breaks arose randomly and that there was no major influence of repeated elements. Non-homologous end-joining appeared as the main mechanism of repair (55% of rearrangements). A diagnosis could be established in 22/49 patients (44.8%), 15 by gene disruption (KANSL1, FOXP1, SPRED1, TLK2, MBD5, DMD, AUTS2, MEIS2, MEF2C, NRXN1, NFIX, SYNGAP1, GHR, ZMIZ1) and 7 by position effect (DLX5, MEF2C, BCL11B, SATB2, ZMIZ1). In addition, 16 new candidate genes were identified. Systematic gene expression studies further supported these results. We also showed the contribution of topologically associated domain maps to WGS data interpretation. CONCLUSION Paired-end WGS is a valid strategy and may be used for structural variation characterisation in a clinical setting.
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Affiliation(s)
- Caroline Schluth-Bolard
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Flavie Diguet
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | | | - Claire Bardel
- Cellule bioinformatique de la plateforme NGS, Hospices Civils de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Lyon 1 University, Bron, France
| | - Alexandra Afenjar
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France.,GRC n°19, pathologies Congénitales du Cervelet-LeucoDystrophies, AP-HP, Hôpital Armand Trousseau, Sorbonne Université, Paris, France
| | - Florence Amblard
- Laboratoire de Génétique Chromosomique, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France
| | - Jeanne Amiel
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Paris, France
| | | | | | - Yline Capri
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | | | | | - Christine Coubes
- Service de Génétique, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Benedicte Demeer
- Centre d'activité de génétique clinique, CLAD nord de France, CHU Amiens, Amiens, France
| | | | | | - Françoise Devillard
- Laboratoire de Génétique Chromosomique, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France
| | | | - Céline Dupont
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Jean-Michel Dupont
- Laboratoire de Cytogénétique Constitutionnelle, APHP-HUPC site Cochin, Paris, France
| | | | - Laurence Faivre
- Centre de référence anomalies du développement et syndromes malformatifs, FHU TRANSLAD et équipe GAD INSERM UMR1231, CHU Dijon-Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | | | | | - Marine Houlier
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Sylvie Jaillard
- Laboratoire de Cytogénétique et de Biologie Cellulaire, CHU Pontchaillou, Rennes, France
| | | | - Valérie Kremer
- Laboratoire de Cytogénétique, CHU Strasbourg, Strasbourg, France
| | - Didier Lacombe
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | | | - Aziza Lebbar
- Laboratoire de Cytogénétique Constitutionnelle, APHP-HUPC site Cochin, Paris, France
| | - Marine Lebrun
- Service de Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, Saint-Etienne, France
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - James Lespinasse
- Laboratoire de Génétique Chromosomique, CH Général, Chambéry, France
| | - Jonathan Levy
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Valérie Malan
- Service de Cytogénétique, Hôpital Necker Enfants Malades, Paris, France
| | | | - Julie Masson
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Alice Masurel-Paulet
- Centre de référence anomalies du développement et syndromes malformatifs, FHU TRANSLAD et équipe GAD INSERM UMR1231, CHU Dijon-Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Cyril Mignot
- Département de Génétique; Centre de Référence Déficience Intellectuelle de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, APHP, Paris, France
| | - Chantal Missirian
- Laboratoire de Génétique Chromosomique, Département de Génétique Médicale, AP-HM, Marseille, France
| | - Fanny Morice-Picard
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Sébastien Moutton
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Gwenaël Nadeau
- Laboratoire de Génétique Chromosomique, CH Général, Chambéry, France.,Service de Cytogénétique, CH Valence, Valence, France
| | - Céline Pebrel-Richard
- Service de Cytogénétique Médicale, Hôpital Estaing, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Sylvie Odent
- Service de Génétique Clinique, CHU Rennes, Rennes, France.,CNRS, IGDR (Institut de Génétique et Développement de Rennes) UMR 6290, Université de Rennes, Rennes, France
| | | | | | - Nicole Philip
- Département de Génétique Médicale, Unité de Génétique Clinique, AP-HM, Marseille, France
| | | | - Linda Pons
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Marie-France Portnoï
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France
| | - Fabienne Prieur
- Service de Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, Saint-Etienne, France
| | | | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Marlène Rio
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Paris, France
| | - Caroline Rooryck-Thambo
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Massimiliano Rossi
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Catherine Sarret
- Service de Génétique Médicale, Hôpital Estaing, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Véronique Satre
- Laboratoire de Génétique Chromosomique, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France.,Equipe Génétique, Epigénétique et Thérapies de l'Infertilité, IAB, INSERM 1209, CNRS UMR5309, Grenoble, France
| | - Jean-Pierre Siffroi
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France
| | - Marianne Till
- Service de Génétique, Hospices Civils de Lyon, Bron, France
| | - Renaud Touraine
- Service de Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, Saint-Etienne, France
| | | | - Jérome Toutain
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Stéphanie Valence
- GRC n°19, pathologies Congénitales du Cervelet-LeucoDystrophies, AP-HP, Hôpital Armand Trousseau, Sorbonne Université, Paris, France.,Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP, GHUEP, Paris, France
| | - Alain Verloes
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Sandra Whalen
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | | | - Damien Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
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15
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Kessi M, Xiong J, Wu L, Yang L, He F, Chen C, Pang N, Duan H, Zhang W, Arafat A, Yin F, Peng J. Rare Copy Number Variations and Predictors in Children With Intellectual Disability and Epilepsy. Front Neurol 2018; 9:947. [PMID: 30510536 PMCID: PMC6252327 DOI: 10.3389/fneur.2018.00947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/23/2018] [Indexed: 11/19/2022] Open
Abstract
Introduction: The concurrence of intellectual disability/global developmental delay and epilepsy (ID/GDD-EP) is very common in the pediatric population. The etiologies for both conditions are complex and largely unknown. The predictors of significant copy number variations (CNVs) are known for the cases with ID/GDD, but unknown for those with exclusive ID/GDD-EP. Importantly, the known predictors are largely from the same ethnic group; hence, they lack replication. Purpose: We aimed to determine and investigate the diagnostic yield of CNV tests, new causative CNVs, and the independent predictors of significant CNVs in Chinese children with unexplained ID/GDD-EP. Materials and methods: A total of 100 pediatric patients with unexplained ID/GDD-EP and 1,000 healthy controls were recruited. The American College of Medical Genetics guideline was used to classify the CNVs. Additionally, clinical information was collected and compared between those with significant and non-significant CNVs. Results: Twenty-eight percent of the patients had significant CNVs, 16% had variants of unknown significance, and 56% had non-significant CNVs. In total, 31 CNVs were identified in 28% (28/100) of cases: 25 pathogenic and 6 likely pathogenic. Eighteen known syndromes were diagnosed in 17 cases. Thirteen rare CNVs (8 novel and 5 reported in literature) were identified, of which three spanned dosage-sensitive genes: 19q13.2 deletion (ATP1A3), Xp11.4-p11.3 deletion (CASK), and 6q25.3-q25.3 deletion (ARID1B). By comparing clinical features in patients with significant CNVs against those with non-significant CNVs, a statistically significant association was found between the presence of significant CNVs and speech and language delay for those aged above 2 years and for those with facial malformations, microcephaly, congenital heart disease, fair skin, eye malformations, and mega cisterna magna. Multivariate logistic regression analysis allowed the identification of two independent significant CNV predictors, which are eye malformations and facial malformations. Conclusion: Our study supports the performance of CNV tests in pediatric patients with unexplained ID/GDD-EP, as there is high diagnostic yield, which informs genetic counseling. It adds 13 rare CNVs (8 novel), which can be accountable for both conditions. Moreover, congenital eye and facial malformations are clinical markers that can aid clinicians to understand which patients can benefit from the CNV testing and which will not, thus helping patients to avoid unnecessary and expensive tests.
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Affiliation(s)
- Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Liwen Wu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Haolin Duan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ahmed Arafat
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
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16
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Abstract
RBFOX3/NeuN is a neuronal splicing regulator involved in neural circuitry balance, as well as neurogenesis and synaptogenesis. Rbfox3 is expressed in neurons; however, in the retina, expression is restricted to cells in the ganglion cell layer and some cells of the inner nuclear layer. Rbfox3 is expressed in a layer-specific manner in the retina, which implies a functional role, however, the role of RBFOX3 in the retina is unknown. Rbfox3 homozygous knockout (Rbfox3-/-) mice exhibit deficits in visual learning; therefore, understanding the role of RBFOX3 in the retina is critical for interpreting behavioral results. We found Rbfox3 expression was developmentally regulated in the retina and specifically expressed in ganglion cells, amacrine cells and horizontal cells of the retina. We demonstrate deletion of Rbfox3 resulted in a reduction in the thickness of the inner plexiform layer of the retina, where synapses are formed. Number of ganglion cells and amacrine cells is normal with loss of Rbfox3. Innervation of retinal ganglion cells into their targeted brain regions is normal in Rbfox3-/- mice. Importantly, Rbfox3-/- mice displayed normal non-image and image forming functions. Taken together, our results suggest RBFOX3 is dispensable for visual function.
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Affiliation(s)
- Yi-Sian Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kuan-Ting Kuo
- Department of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Kuo Chen
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- Neurodevelopmental Club in Taiwan, Taipei, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Neurodevelopmental Club in Taiwan, Taipei, Taiwan
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17
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Papadopoulou Z, Papoulidis I, Sifakis S, Markopoulos G, Vetro A, Vlaikou AM, Ziegler M, Liehr T, Thomaidis L, Zuffardi O, Syrrou M, George K, Manolakos E. Partial monosomy 8p and trisomy 16q in two children with developmental delay detected by array comparative genomic hybridization. Mol Med Rep 2017; 16:8808-8818. [PMID: 29039589 PMCID: PMC5779959 DOI: 10.3892/mmr.2017.7760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Two cases of liveborn unrelated children with developmental delay and overlapping unbalanced translocations der(8)t(8;16)(p23.2;q23.3) and der (8)t(8;16)(p23.1;q23.1), leading to partial monosomy 8p and partial trisomy 16q, are reported in the present study. The first patient was a 10-year-old boy with mild developmental delay and minor congenital anomalies (borderline microcephaly, clinodactyly, hypertelorism, epicanthus, mild systolic murmur and kidney reflux). The second patient was a 3 year-old girl with developmental delay, gross motor milestone delay and dysmorphic features. Array-comparative genomic hybridization analysis revealed that partial chromosome 8p monosomy extended from 8p23.2 to 8pter (4.8 Mb) in Patient 1 and from 8p23.1 to 8pter (9.5 Mb) in Patient 2, and partial chromosome 16 trisomy extended from 16q23.3 to 16qter (5.6 Mb) in Patient 1 and from 16q23.1 to 16qter (11.7 Mb) in Patient 2. The mechanism of appearance of the rearrangement in association with the genes involved and the architecture of the region is discussed.
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Affiliation(s)
- Zoe Papadopoulou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
| | - Ioannis Papoulidis
- Access To Genome, Laboratory of Genetics, Athens 11528‑Thessaloniki 55134, Greece
| | - Stavros Sifakis
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, Heraklion 71201, Greece
| | - Georgios Markopoulos
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
| | - Annalisa Vetro
- Department of Molecular Medicine, University of Pavia, I‑27100 Pavia, Italy
| | - Angeliki-Maria Vlaikou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
| | - Monica Ziegler
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D‑07743 Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, D‑07743 Jena, Germany
| | - Loretta Thomaidis
- Developmental Assessment Unit, 2nd Department of Pediatrics, P. & A. Kyriakou Children's Hospital, National and Kapodistrian University of Athens School of Medicine, Athens 11527, Greece
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, I‑27100 Pavia, Italy
| | - Maria Syrrou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina 45110, Greece
| | - Kitsos George
- Department of Ophthalmology, University of Ioannina, Ioannina 45110, Greece
| | - Emmanouil Manolakos
- Access To Genome, Laboratory of Genetics, Athens 11528‑Thessaloniki 55134, Greece
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18
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Aksoy I, Utami KH, Winata CL, Hillmer AM, Rouam SL, Briault S, Davila S, Stanton LW, Cacheux V. Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in neurodevelopmental disorders. Hum Mol Genet 2017; 26:367-382. [PMID: 28365779 DOI: 10.1093/hmg/ddw393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/11/2016] [Indexed: 01/22/2023] Open
Abstract
The cellular and molecular mechanisms underlying neurodevelopmental conditions such as autism spectrum disorders have been studied intensively for decades. The ability to generate patient-specific induced pluripotent stem cells (iPSCs) now offers a novel strategy for modelling human diseases. Recent studies have reported the derivation of iPSCs from patients with neurological disorders. The key challenge remains the demonstration of disease-related phenotypes and the ability to model the disease. Here we report a case study with signs of neurodevelopmental disorders (NDDs) harbouring chromosomal rearrangements that were sequenced using long-insert DNA paired-end tag (DNA-PET) sequencing approach. We identified the disruption of a specific gene, GTDC1. By deriving iPSCs from this patient and differentiating them into neural progenitor cells (NPCs) and neurons we dissected the disease process at the cellular level and observed defects in both NPCs and neuronal cells. We also showed that disruption of GTDC1 expression in wild type human NPCs and neurons showed a similar phenotype as patient's iPSCs. Finally, we utilized a zebrafish model to demonstrate a role for GTDC1 in the development of the central nervous system. Our findings highlight the importance of combining sequencing technologies with the iPSC technology for NDDs modelling that could be applied for personalized medicine.
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Affiliation(s)
- Irene Aksoy
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore.,University of Lyon, University Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Kagistia H Utami
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore
| | - Cecilia L Winata
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore.,International Institute of Molecular and Cell Biology, Warsaw, Poland.,Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Axel M Hillmer
- Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore
| | - Sigrid L Rouam
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore
| | - Sylvain Briault
- Service de Génétique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d'Orléans, Orléans, France
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, 60 Biopolis Street, Singapore, Singapore
| | - Lawrence W Stanton
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore.,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Valere Cacheux
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore
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19
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Wang Z, Henn BC, Wang C, Wei Y, Su L, Sun R, Chen H, Wagner PJ, Lu Q, Lin X, Wright R, Bellinger D, Kile M, Mazumdar M, Tellez-Rojo MM, Schnaas L, Christiani DC. Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment. Environ Health 2017; 16:81. [PMID: 28754176 PMCID: PMC5534076 DOI: 10.1186/s12940-017-0288-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 07/17/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Neurodevelopment is a complex process involving both genetic and environmental factors. Prenatal exposure to lead (Pb) has been associated with lower performance on neurodevelopmental tests. Adverse neurodevelopmental outcomes are more frequent and/or more severe when toxic exposures interact with genetic susceptibility. METHODS To explore possible loci associated with increased susceptibility to prenatal Pb exposure, we performed a genome-wide gene-environment interaction study (GWIS) in young children from Mexico (n = 390) and Bangladesh (n = 497). Prenatal Pb exposure was estimated by cord blood Pb concentration. Neurodevelopment was assessed using the Bayley Scales of Infant Development. RESULTS We identified a locus on chromosome 8, containing UNC5D, and demonstrated evidence of its genome-wide significance with mental composite scores (rs9642758, p meta = 4.35 × 10-6). Within this locus, the joint effects of two independent single nucleotide polymorphisms (SNPs, rs9642758 and rs10503970) had a p-value of 4.38 × 10-9 for mental composite scores. Correlating GWIS results with in vitro transcriptomic profiles identified one common gene, SLC1A5, which is involved in synaptic function, neuronal development, and excitotoxicity. Further analysis revealed interconnected interactions that formed a large network of 52 genes enriched with oxidative stress genes and neurodevelopmental genes. CONCLUSIONS Our findings suggest that certain genetic polymorphisms within/near genes relevant to neurodevelopment might modify the toxic effects of Pb exposure via oxidative stress.
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Affiliation(s)
- Zhaoxi Wang
- Harvard TH Chan School of Public Health, Boston, MA USA
| | - Birgit Claus Henn
- Department of Environmental Health, Boston University, School of Public Health, Boston, USA
| | | | - Yongyue Wei
- Department of Epidemiology, Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Su
- Harvard TH Chan School of Public Health, Boston, MA USA
| | - Ryan Sun
- Harvard TH Chan School of Public Health, Boston, MA USA
| | - Han Chen
- Harvard TH Chan School of Public Health, Boston, MA USA
| | | | - Quan Lu
- Harvard TH Chan School of Public Health, Boston, MA USA
| | - Xihong Lin
- Harvard TH Chan School of Public Health, Boston, MA USA
| | | | - David Bellinger
- Harvard TH Chan School of Public Health, Boston, MA USA
- Children’s Hospital Boston, Boston, USA
| | | | - Maitreyi Mazumdar
- Harvard TH Chan School of Public Health, Boston, MA USA
- Children’s Hospital Boston, Boston, USA
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20
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Vlaskamp DRM, Callenbach PMC, Rump P, Giannini LAA, Dijkhuizen T, Brouwer OF, van Ravenswaaij-Arts CMA. Copy number variation in a hospital-based cohort of children with epilepsy. Epilepsia Open 2017; 2:244-254. [PMID: 29588953 PMCID: PMC5719854 DOI: 10.1002/epi4.12057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 01/15/2023] Open
Abstract
Objective To evaluate the diagnostic yield of microarray analysis in a hospital‐based cohort of children with seizures and to identify novel candidate genes and susceptibility loci for epilepsy. Methods Of all children who presented with their first seizure in the University Medical Center Groningen (January 2000 through May 2013) (n = 1,368), we included 226 (17%) children who underwent microarray analysis before June 2014. All 226 children had a definite diagnosis of epilepsy. All their copy number variants (CNVs) on chromosomes 1–22 and X that contain protein‐coding genes and have a prevalence of <1% in healthy controls were evaluated for their pathogenicity. Results Children selected for microarray analysis more often had developmental problems (82% vs. 25%, p < 0.001), facial dysmorphisms (49% vs. 8%, p < 0.001), or behavioral problems (41% vs. 13%, p < 0.001) than children who were not selected. We found known clinically relevant CNVs for epilepsy in 24 of the 226 children (11%). Seventeen of these 24 children had been diagnosed with symptomatic focal epilepsy not otherwise specified (71%) and five with West syndrome (21%). Of these 24 children, many had developmental problems (100%), behavioral problems (54%) or facial dysmorphisms (46%). We further identified five novel CNVs comprising four potential candidate genes for epilepsy: MYT1L, UNC5D, SCN4B, and NRXN3. Significance The 11% yield in our hospital‐based cohort underscores the importance of microarray analysis in diagnostic evaluation of children with epilepsy.
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Affiliation(s)
- Danique R M Vlaskamp
- Departments of Neurology University Medical Center Groningen University of Groningen Groningen the Netherlands.,Department of Genetics University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - Petra M C Callenbach
- Departments of Neurology University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - Patrick Rump
- Department of Genetics University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - Lucia A A Giannini
- Department of Genetics University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - Trijnie Dijkhuizen
- Department of Genetics University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - Oebele F Brouwer
- Departments of Neurology University Medical Center Groningen University of Groningen Groningen the Netherlands
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21
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Aristidou C, Koufaris C, Theodosiou A, Bak M, Mehrjouy MM, Behjati F, Tanteles G, Christophidou-Anastasiadou V, Tommerup N, Sismani C. Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing. PLoS One 2017; 12:e0169935. [PMID: 28072833 DOI: 10.1371/journal.pone.0169935] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
Familial apparently balanced translocations (ABTs) segregating with discordant phenotypes are extremely challenging for interpretation and counseling due to the scarcity of publications and lack of routine techniques for quick investigation. Recently, next generation sequencing has emerged as an efficacious methodology for precise detection of translocation breakpoints. However, studies so far have mainly focused on de novo translocations. The present study focuses specifically on familial cases in order to shed some light to this diagnostic dilemma. Whole-genome mate-pair sequencing (WG-MPS) was applied to map the breakpoints in nine two-way ABT carriers from four families. Translocation breakpoints and patient-specific structural variants were validated by Sanger sequencing and quantitative Real Time PCR, respectively. Identical sequencing patterns and breakpoints were identified in affected and non-affected members carrying the same translocations. PTCD1, ATP5J2-PTCD1, CADPS2, and STPG1 were disrupted by the translocations in three families, rendering them initially as possible disease candidate genes. However, subsequent mutation screening and structural variant analysis did not reveal any pathogenic mutations or unique variants in the affected individuals that could explain the phenotypic differences between carriers of the same translocations. In conclusion, we suggest that NGS-based methods, such as WG-MPS, can be successfully used for detailed mapping of translocation breakpoints, which can also be used in routine clinical investigation of ABT cases. Unlike de novo translocations, no associations were determined here between familial two-way ABTs and the phenotype of the affected members, in which the presence of cryptic imbalances and complex chromosomal rearrangements has been excluded. Future whole-exome or whole-genome sequencing will potentially reveal unidentified mutations in the patients underlying the discordant phenotypes within each family. In addition, larger studies are needed to determine the exact percentage for phenotypic risk in families with ABTs.
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22
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Redin C, Brand H, Collins RL, Kammin T, Mitchell E, Hodge JC, Hanscom C, Pillalamarri V, Seabra CM, Abbott MA, Abdul-Rahman OA, Aberg E, Adley R, Alcaraz-Estrada SL, Alkuraya FS, An Y, Anderson MA, Antolik C, Anyane-Yeboa K, Atkin JF, Bartell T, Bernstein JA, Beyer E, Blumenthal I, Bongers EM, Brilstra EH, Brown CW, Brüggenwirth HT, Callewaert B, Chiang C, Corning K, Cox H, Cuppen E, Currall BB, Cushing T, David D, Deardorff MA, Dheedene A, D'Hooghe M, de Vries BB, Earl DL, Ferguson HL, Fisher H, FitzPatrick DR, Gerrol P, Giachino D, Glessner JT, Gliem T, Grady M, Graham BH, Griffis C, Gripp KW, Gropman AL, Hanson-Kahn A, Harris DJ, Hayden MA, Hill R, Hochstenbach R, Hoffman JD, Hopkin RJ, Hubshman MW, Innes AM, Irons M, Irving M, Jacobsen JC, Janssens S, Jewett T, Johnson JP, Jongmans MC, Kahler SG, Koolen DA, Korzelius J, Kroisel PM, Lacassie Y, Lawless W, Lemyre E, Leppig K, Levin AV, Li H, Li H, Liao EC, Lim C, Lose EJ, Lucente D, Macera MJ, Manavalan P, Mandrile G, Marcelis CL, Margolin L, Mason T, Masser-Frye D, McClellan MW, Mendoza CJ, Menten B, Middelkamp S, Mikami LR, Moe E, Mohammed S, Mononen T, Mortenson ME, Moya G, Nieuwint AW, Ordulu Z, Parkash S, Pauker SP, Pereira S, Perrin D, Phelan K, Aguilar RE, Poddighe PJ, Pregno G, Raskin S, Reis L, Rhead W, Rita D, Renkens I, Roelens F, Ruliera J, Rump P, Schilit SL, Shaheen R, Sparkes R, Spiegel E, Stevens B, Stone MR, Tagoe J, Thakuria JV, van Bon BW, van de Kamp J, van Der Burgt I, van Essen T, van Ravenswaaij-Arts CM, van Roosmalen MJ, Vergult S, Volker-Touw CM, Warburton DP, Waterman MJ, Wiley S, Wilson A, Yerena-de Vega MC, Zori RT, Levy B, Brunner HG, de Leeuw N, Kloosterman WP, Thorland EC, Morton CC, Gusella JF, Talkowski ME. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nat Genet 2017; 49:36-45. [PMID: 27841880 DOI: 10.1038/ng.3720] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/17/2016] [Indexed: 12/16/2022]
Abstract
Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology.
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23
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Lin YS, Wang HY, Huang DF, Hsieh PF, Lin MY, Chou CH, Wu IJ, Huang GJ, Gau SSF, Huang HS. Neuronal Splicing Regulator RBFOX3 (NeuN) Regulates Adult Hippocampal Neurogenesis and Synaptogenesis. PLoS One 2016; 11:e0164164. [PMID: 27701470 PMCID: PMC5049801 DOI: 10.1371/journal.pone.0164164] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
Dysfunction of RBFOX3 has been identified in neurodevelopmental disorders such as autism spectrum disorder, cognitive impairments and epilepsy and a causal relationship with these diseases has been previously demonstrated with Rbfox3 homozygous knockout mice. Despite the importance of RBFOX3 during neurodevelopment, the function of RBFOX3 regarding neurogenesis and synaptogenesis remains unclear. To address this critical question, we profiled the developmental expression pattern of Rbfox3 in the brain of wild-type mice and analyzed brain volume, disease-relevant behaviors, neurogenesis, synaptic plasticity, and synaptogenesis in Rbfox3 homozygous knockout mice and their corresponding wild-type counterparts. Here we report that expression of Rbfox3 differs developmentally for distinct brain regions. Moreover, Rbfox3 homozygous knockout mice exhibited cold hyperalgesia and impaired cognitive abilities. Focusing on hippocampal phenotypes, we found Rbfox3 homozygous knockout mice displayed deficits in neurogenesis, which was correlated with cognitive impairments. Furthermore, RBFOX3 regulates the exons of genes with synapse-related function. Synaptic plasticity and density, which are related to cognitive behaviors, were altered in the hippocampal dentate gyrus of Rbfox3 homozygous knockout mice; synaptic plasticity decreased and the density of synapses increased. Taken together, our results demonstrate the important role of RBFOX3 during neural development and maturation. In addition, abnormalities in synaptic structure and function occur in Rbfox3 homozygous knockout mice. Our findings may offer mechanistic explanations for human brain diseases associated with dysfunctional RBFOX3.
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Affiliation(s)
- Yi-Sian Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Han-Ying Wang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - De-Fong Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Fen Hsieh
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Ying Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Hsuan Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Ju Wu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Guo-Jen Huang
- Department of Biomedical Sciences, Chang Gung University, Tao-Yuan, Taiwan
| | - Susan Shur-Fen Gau
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Neurodevelopment Club in Taiwan, Taipei, Taiwan
- * E-mail:
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Amin N, Allebrandt KV, van der Spek A, Müller-Myhsok B, Hek K, Teder-Laving M, Hayward C, Esko T, van Mill JG, Mbarek H, Watson NF, Melville SA, Del Greco FM, Byrne EM, Oole E, Kolcic I, Chen TH, Evans DS, Coresh J, Vogelzangs N, Karjalainen J, Willemsen G, Gharib SA, Zgaga L, Mihailov E, Stone KL, Campbell H, Brouwer RWW, Demirkan A, Isaacs A, Dogas Z, Marciante KD, Campbell S, Borovecki F, Luik AI, Li M, Hottenga JJ, Huffman JE, van den Hout MCGN, Cummings SR, Aulchenko YS, Gehrman PR, Uitterlinden AG, Wichmann HE, Müller-Nurasyid M, Fehrmann RSN, Montgomery GW, Hofman A, Kao WHL, Oostra BA, Wright AF, Vink JM, Wilson JF, Pramstaller PP, Hicks AA, Polasek O, Punjabi NM, Redline S, Psaty BM, Heath AC, Merrow M, Tranah GJ, Gottlieb DJ, Boomsma DI, Martin NG, Rudan I, Tiemeier H, van IJcken WFJ, Penninx BW, Metspalu A, Meitinger T, Franke L, Roenneberg T, van Duijn CM. Genetic variants in RBFOX3 are associated with sleep latency. Eur J Hum Genet 2016; 24:1488-95. [PMID: 27142678 PMCID: PMC5027680 DOI: 10.1038/ejhg.2016.31] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/13/2016] [Accepted: 02/01/2016] [Indexed: 01/30/2023] Open
Abstract
Time to fall asleep (sleep latency) is a major determinant of sleep quality. Chronic, long sleep latency is a major characteristic of sleep-onset insomnia and/or delayed sleep phase syndrome. In this study we aimed to discover common polymorphisms that contribute to the genetics of sleep latency. We performed a meta-analysis of genome-wide association studies (GWAS) including 2 572 737 single nucleotide polymorphisms (SNPs) established in seven European cohorts including 4242 individuals. We found a cluster of three highly correlated variants (rs9900428, rs9907432 and rs7211029) in the RNA-binding protein fox-1 homolog 3 gene (RBFOX3) associated with sleep latency (P-values=5.77 × 10(-08), 6.59 × 10(-)(08) and 9.17 × 10(-)(08)). These SNPs were replicated in up to 12 independent populations including 30 377 individuals (P-values=1.5 × 10(-)(02), 7.0 × 10(-)(03) and 2.5 × 10(-)(03); combined meta-analysis P-values=5.5 × 10(-07), 5.4 × 10(-07) and 1.0 × 10(-07)). A functional prediction of RBFOX3 based on co-expression with other genes shows that this gene is predominantly expressed in brain (P-value=1.4 × 10(-316)) and the central nervous system (P-value=7.5 × 10(-)(321)). The predicted function of RBFOX3 based on co-expression analysis with other genes shows that this gene is significantly involved in the release cycle of neurotransmitters including gamma-aminobutyric acid and various monoamines (P-values<2.9 × 10(-11)) that are crucial in triggering the onset of sleep. To conclude, in this first large-scale GWAS of sleep latency we report a novel association of variants in RBFOX3 gene. Further, a functional prediction of RBFOX3 supports the involvement of RBFOX3 with sleep latency.
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Affiliation(s)
- Najaf Amin
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Karla V Allebrandt
- Institute of Medical Psychology, Ludwig-Maximilians-University, Munich, Germany
| | - Ashley van der Spek
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | | | - Karin Hek
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Maris Teder-Laving
- Estonian Genome Center, University of Tartu and Estonian Biocenter, Tartu, Estonia
| | - Caroline Hayward
- Medical Research Council, Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu and Estonian Biocenter, Tartu, Estonia
| | - Josine G van Mill
- Department of Psychiatry, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Hamdi Mbarek
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Nathaniel F Watson
- Department of Neurology, University of Washington, Seattle, WA, USA
- University of Washington Medicine Sleep Center, Seattle, WA, USA
| | - Scott A Melville
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Fabiola M Del Greco
- Center for Biomedicine, European Academy of Bolzano, Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Enda M Byrne
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Edwin Oole
- Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ivana Kolcic
- School of Medicine, University of Split, Split, Croatia
| | - Ting-hsu Chen
- VA Boston Healthcare System, Boston University, Boston, MA, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Josef Coresh
- Departments of Epidemiology, Biostatistics, and Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nicole Vogelzangs
- Department of Psychiatry, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Juha Karjalainen
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Sina A Gharib
- University of Washington Medicine Sleep Center, Seattle, WA, USA
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, University of Washington, Seattle, WA, USA
| | - Lina Zgaga
- Medical Research Council, Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu and Estonian Biocenter, Tartu, Estonia
| | - Katie L Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Rutger WW Brouwer
- Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ayse Demirkan
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Aaron Isaacs
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Zoran Dogas
- Department of Neuroscience and Sleep Medicine Centre, University of Split School of Medicine, Split, Croatia
| | - Kristin D Marciante
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Susan Campbell
- Medical Research Council, Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland
| | - Fran Borovecki
- Centre for Functional Genomics and Department of Neurology, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Annemarie I Luik
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Man Li
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Jouke Jan Hottenga
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Jennifer E Huffman
- Medical Research Council, Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland
| | | | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Yurii S Aulchenko
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Philip R Gehrman
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing and National Genomics Initiative, Leiden, The Netherlands
| | - Heinz-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University and Klinikum Grosshadern, Munich, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - Martina Müller-Nurasyid
- Institute of Epidemiology I, Helmholtz Zentrum Munich-German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Rudolf SN Fehrmann
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | | | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Wen Hong Linda Kao
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Ben A Oostra
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Alan F Wright
- Medical Research Council, Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland
| | - Jacqueline M Vink
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - James F Wilson
- Medical Research Council, Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, Scotland
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy of Bolzano, Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Center for Biomedicine, European Academy of Bolzano, Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Ozren Polasek
- School of Medicine, University of Split, Split, Croatia
- Centre for Global Health, University of Split School of Medicine, Split, Croatia
| | - Naresh M Punjabi
- Department of Pulmonary Medicine and Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital and Beth Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University, St Louis, MO, USA
| | - Martha Merrow
- Institute of Medical Psychology, Ludwig-Maximilians-University, Munich, Germany
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Daniel J Gottlieb
- Department of Medicine, Brigham and Women's Hospital and Beth Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | | | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | | | - Brenda W Penninx
- Department of Psychiatry, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu and Estonian Biocenter, Tartu, Estonia
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Techinsche Universität München, München, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Till Roenneberg
- Institute of Medical Psychology, Ludwig-Maximilians-University, Munich, Germany
| | - Cornelia M van Duijn
- Unit of Genetic Epidemiology, Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing and National Genomics Initiative, Leiden, The Netherlands
- Centre for Medical Systems Biology, Leiden, The Netherlands
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Burnett RM, Craven KE, Krishnamurthy P, Goswami CP, Badve S, Crooks P, Mathews WP, Bhat-Nakshatri P, Nakshatri H. Organ-specific adaptive signaling pathway activation in metastatic breast cancer cells. Oncotarget 2016; 6:12682-96. [PMID: 25926557 PMCID: PMC4494966 DOI: 10.18632/oncotarget.3707] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/10/2015] [Indexed: 01/18/2023] Open
Abstract
Breast cancer metastasizes to bone, visceral organs, and/or brain depending on the subtype, which may involve activation of a host organ-specific signaling network in metastatic cells. To test this possibility, we determined gene expression patterns in MDA-MB-231 cells and its mammary fat pad tumor (TMD-231), lung-metastasis (LMD-231), bone-metastasis (BMD-231), adrenal-metastasis (ADMD-231) and brain-metastasis (231-BR) variants. When gene expression between metastases was compared, 231-BR cells showed the highest gene expression difference followed by ADMD-231, LMD-231, and BMD-231 cells. Neuronal transmembrane proteins SLITRK2, TMEM47, and LYPD1 were specifically overexpressed in 231-BR cells. Pathway-analyses revealed activation of signaling networks that would enable cancer cells to adapt to organs of metastasis such as drug detoxification/oxidative stress response/semaphorin neuronal pathway in 231-BR, Notch/orphan nuclear receptor signals involved in steroidogenesis in ADMD-231, acute phase response in LMD-231, and cytokine/hematopoietic stem cell signaling in BMD-231 cells. Only NF-κB signaling pathway activation was common to all except BMD-231 cells. We confirmed NF-κB activation in 231-BR and in a brain metastatic variant of 4T1 cells (4T1-BR). Dimethylaminoparthenolide inhibited NF-κB activity, LYPD1 expression, and proliferation of 231-BR and 4T1-BR cells. Thus, transcriptome change enabling adaptation to host organs is likely one of the mechanisms associated with organ-specific metastasis and could potentially be targeted therapeutically.
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Affiliation(s)
- Riesa M Burnett
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kelly E Craven
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Purna Krishnamurthy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chirayu P Goswami
- Department of Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sunil Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | | | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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26
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Hahn YK, Masvekar RR, Xu R, Hauser KF, Knapp PE. Chronic HIV-1 Tat and HIV reduce Rbfox3/NeuN: evidence for sex-related effects. Curr HIV Res 2015; 13:10-20. [PMID: 25760045 DOI: 10.2174/1570162x13666150311163733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/17/2014] [Accepted: 02/13/2015] [Indexed: 11/22/2022]
Abstract
The NeuN antibody has been widely used to identify and quantify neurons in normal and disease situations based on binding to a nuclear epitope in most types of neurons. This epitope was recently identified as the RNA-binding, feminizing locus on X-3 (Rbfox3), a member of the larger, mammalian Fox1 family of RNA binding proteins. Fox1 proteins recognize a unique UGCAUG mRNA motif and regulate alternative splicing of precursor mRNA to control post-transcriptional events important in neuronal differentiation and central nervous system development. Recent clinical findings show that Rbfox3/NeuN gene dosage is altered in certain human neurodevelopmental disorders, and redistribution has been noted in HIV(+) tissue. We hypothesized that HIV-1 Tat might affect Rbfox3/NeuN expression, and examined this question in vivo using inducible transgenic mice, and in vitro using human mesencephalic-derived neurons. Rbfox3/NeuN expression and localization in HIV+ basal ganglia and hippocampus was also examined. Chronic Tat exposure reduced Rbfox3/NeuN protein levels and increased cytoplasmic localization, similar to the effect of HIV exposure. Cytoplasmic Rbfox3/NeuN signal has occasionally been reported, although the meaning or function of cytoplasmic versus nuclear localization remains speculative. Importantly, Rbfox3/NeuN reductions were more significant in male mice. Although Rbfox3/NeuN-expressing cells were significantly decreased by Tat exposure, stereology showed that Nissl(+) neuron numbers remained normal. Thus, loss of Rbfox3/NeuN may relate more to functional change than to neuron loss. The effects of Tat by itself are highly relevant to HIV(+) individuals maintained on antiretroviral therapy, since Tat is released from infected cells even when viral replication is inhibited.
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Affiliation(s)
- Yun Kyung Hahn
- Department of Anatomy & Neurobiology, MCV Campus, Virginia Commonwealth University, P.O. Box 980709, Richmond, VA 23298-0709, USA.
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27
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Wang HY, Hsieh PF, Huang DF, Chin PS, Chou CH, Tung CC, Chen SY, Lee LJ, Gau SS, Huang HS. RBFOX3/NeuN is Required for Hippocampal Circuit Balance and Function. Sci Rep 2015; 5:17383. [PMID: 26619789 DOI: 10.1038/srep17383] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/14/2015] [Indexed: 11/08/2022] Open
Abstract
RBFOX3 mutations are linked to epilepsy and cognitive impairments, but the underlying pathophysiology of these disorders is poorly understood. Here we report replication of human symptoms in a mouse model with disrupted Rbfox3. Rbfox3 knockout mice displayed increased seizure susceptibility and decreased anxiety-related behaviors. Focusing on hippocampal phenotypes, we found Rbfox3 knockout mice showed increased expression of plasticity genes Egr4 and Arc, and the synaptic transmission and plasticity were defective in the mutant perforant pathway. The mutant dentate granules cells exhibited an increased frequency, but normal amplitude, of excitatory synaptic events, and this change was associated with an increase in the neurotransmitter release probability and dendritic spine density. Together, our results demonstrate anatomical and functional abnormality in Rbfox3 knockout mice, and may provide mechanistic insights for RBFOX3-related human brain disorders.
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28
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Schneider A, Puechberty J, Ng BL, Coubes C, Gatinois V, Tournaire M, Girard M, Dumont B, Bouret P, Magnetto J, Baghdadli A, Pellestor F, Geneviève D. Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder. Am J Med Genet A 2015; 167A:3031-7. [PMID: 26333717 DOI: 10.1002/ajmg.a.37350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/12/2015] [Indexed: 11/09/2022]
Abstract
Intellectual disability (ID) is a frequent feature but is highly clinically and genetically heterogeneous. The establishment of the precise diagnosis in patients with ID is challenging due to this heterogeneity but crucial for genetic counseling and appropriate care for the patients. Among the etiologies of patients with ID, apparently balanced de novo rearrangements represent 0.6%. Several mechanisms explain the ID in patients with apparently balanced de novo rearrangement. Among them, disruption of a disease gene at the breakpoint, is frequently evoked. In this context, technologies recently developed are used to characterize precisely such chromosomal rearrangements. Here, we report the case of a boy with ID, facial features and autistic behavior who is carrying a de novo balanced reciprocal translocation t(3;7)(q11.2;q11.22)dn. Using microarray analysis, array painting (AP) technology combined with molecular study, we have identified the interruption of the autism susceptibility candidate 2 gene (AUTS2) and EPH receptor A6 gene (EPHA6). We consider that the disruption of AUTS2 explains the phenotype of the patient; the exact role of EPHA6 in human pathology is not well defined. Based on the observation of recurrent germinal and somatic translocations involving AUTS2 and the molecular environment content, we put forward the hypothesis that the likely chromosomal mechanism responsible for the translocation could be due either to replicative stress or to recombination-based mechanisms.
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Affiliation(s)
- Anouck Schneider
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | | | - Bee Ling Ng
- Cytometry Core Facility, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Vincent Gatinois
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Magali Tournaire
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Manon Girard
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Bruno Dumont
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Pauline Bouret
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Julia Magnetto
- CRA, Département de Psychiatrie de l'Enfant et de l'Adolescent, Centre de Ressources Autisme, CHRU de Montpellier, France
| | - Amaria Baghdadli
- CRA, Département de Psychiatrie de l'Enfant et de l'Adolescent, Centre de Ressources Autisme, CHRU de Montpellier, France
| | - Franck Pellestor
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - David Geneviève
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France.,Département de Génétique Médicale, CHRU de Montpellier, France
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29
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Abstract
Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation.
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Affiliation(s)
- Brooke Weckselblatt
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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30
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Abstract
Polymorphic inversions are a type of structural variants that are difficult to analyze owing to their balanced nature and the location of breakpoints within complex repeated regions. So far, only a handful of inversions have been studied in detail in humans and current knowledge about their possible functional effects is still limited. However, inversions have been related to phenotypic changes and adaptation in multiple species. In this review, we summarize the evidences of the functional impact of inversions in the human genome. First, given that inversions have been shown to inhibit recombination in heterokaryotes, chromosomes displaying different orientation are expected to evolve independently and this may lead to distinct gene-expression patterns. Second, inversions have a role as disease-causing mutations both by directly affecting gene structure or regulation in different ways, and by predisposing to other secondary arrangements in the offspring of inversion carriers. Finally, several inversions show signals of being selected during human evolution. These findings illustrate the potential of inversions to have phenotypic consequences also in humans and emphasize the importance of their inclusion in genome-wide association studies.
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31
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Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, Deng X. Escape from X inactivation varies in mouse tissues. PLoS Genet 2015; 11:e1005079. [PMID: 25785854 PMCID: PMC4364777 DOI: 10.1371/journal.pgen.1005079] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/17/2015] [Indexed: 12/22/2022] Open
Abstract
X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape genes in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a binomial model to assess allelic expression, we demonstrate a continuum between complete silencing and expression from the inactive X (Xi). The validity of the RNA-seq approach was verified using RT-PCR with species-specific primers or Sanger sequencing. Both common escape genes and genes with significant differences in XCI status between tissues were identified. Such genes may be candidates for tissue-specific sex differences. Overall, few genes (3-7%) escape XCI in any of the mouse tissues examined, suggesting stringent silencing and escape controls. In contrast, an in vitro system represented by the embryonic-kidney-derived Patski cell line showed a higher density of escape genes (21%), representing both kidney-specific escape genes and cell-line specific escape genes. Allele-specific RNA polymerase II occupancy and DNase I hypersensitivity at the promoter of genes on the Xi correlated well with levels of escape, consistent with an open chromatin structure at escape genes. Allele-specific CTCF binding on the Xi clustered at escape genes and was denser in brain compared to the Patski cell line, possibly contributing to a more compartmentalized structure of the Xi and fewer escape genes in brain compared to the cell line where larger domains of escape were observed.
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Affiliation(s)
- Joel B. Berletch
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Wenxiu Ma
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Fan Yang
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Christine M. Disteche
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Xinxian Deng
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
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Duan W, Zhang YP, Hou Z, Huang C, Zhu H, Zhang CQ, Yin Q. Novel Insights into NeuN: from Neuronal Marker to Splicing Regulator. Mol Neurobiol 2015; 53:1637-1647. [PMID: 25680637 DOI: 10.1007/s12035-015-9122-5] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/01/2015] [Indexed: 01/07/2023]
Abstract
Neuronal nuclei (NeuN) is a well-recognized "marker" that is detected exclusively in post-mitotic neurons and was initially identified through an immunological screen to produce neuron-specific antibodies. Immunostaining evidence indicates that NeuN is distributed in the nuclei of mature neurons in nearly all parts of the vertebrate nervous system. NeuN is highly conserved among species and is stably expressed during specific stages of development. Therefore, NeuN has been considered to be a reliable marker of mature neurons for the past two decades. However, this role has been challenged by recent studies indicating that NeuN staining is variable and even absent during certain diseases and specific physiological states. More importantly, despite the widespread use of the anti-NeuN antibody, the natural identity of the NeuN protein remained elusive for 17 years. NeuN was recently eventually identified as an epitope of Rbfox3, which is a novel member of the Rbfox1 family of splicing factors. This identification might provide a novel perspective on NeuN expression during both physiological and pathological conditions. This review summarizes the current progress on the biochemical identity and biological significance of NeuN and recommends caution when applying NeuN immunoreactivity as a definitive marker of mature neurons in certain diseases and specific physiological states.
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Affiliation(s)
- Wei Duan
- Department of Neurology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China
| | - Yu-Ping Zhang
- Department of Pediatrics, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China
| | - Zhi Hou
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China
| | - Chen Huang
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - He Zhu
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA.,Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.,The Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN, 37232, USA
| | - Chun-Qing Zhang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China.
| | - Qing Yin
- Department of Rehabilitation and Physical Therapy, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Suzuki T, Tsurusaki Y, Nakashima M, Miyake N, Saitsu H, Takeda S, Matsumoto N. Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing. J Hum Genet 2014; 59:649-54. [PMID: 25296578 DOI: 10.1038/jhg.2014.88] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/09/2022]
Abstract
Structural variations (SVs), including translocations, inversions, deletions and duplications, are potentially associated with Mendelian diseases and contiguous gene syndromes. Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). These data indicate the efficacy of WGS for the precise determination of translocation and inversion breakpoints.
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