1
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Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
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2
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Czakó M, Till Á, Zima J, Zsigmond A, Szabó A, Maász A, Melegh B, Hadzsiev K. Xp11.2 Duplication in Females: Unique Features of a Rare Copy Number Variation. Front Genet 2021; 12:635458. [PMID: 33936165 PMCID: PMC8080037 DOI: 10.3389/fgene.2021.635458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Among the diseases with X-linked inheritance and intellectual disability, duplication of the Xp11.23p11.22 region is indeed a rare phenomenon, with less than 90 cases known in the literature. Most of them have been recognized with the routine application of array techniques, as these copy number variations (CNVs) are highly variable in size, occurring in recurrent and non-recurrent forms. Its pathogenic role is not debated anymore, but the information available about the pathomechanism, especially in affected females, is still very limited. It has been observed that the phenotype in females varies from normal to severe, which does not correlate with the size of the duplication or the genes involved, and which makes it very difficult to give an individual prognosis. Among the patients studied by the authors because of intellectual disability, epilepsy, and minor anomalies, overlapping duplications affecting the Xp11.23p11.22 region were detected in three females. Based on our detailed phenotype analysis, we concluded that Xp11.23p11.22 duplication is a neurodevelopmental disorder.
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Affiliation(s)
- Márta Czakó
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Ágnes Till
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | - Judith Zima
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | - Anna Zsigmond
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | - András Szabó
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Anita Maász
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Béla Melegh
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
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3
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Wilkinson E, Cui YH, He YY. Context-Dependent Roles of RNA Modifications in Stress Responses and Diseases. Int J Mol Sci 2021; 22:ijms22041949. [PMID: 33669361 PMCID: PMC7920320 DOI: 10.3390/ijms22041949] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
RNA modifications are diverse post-transcriptional modifications that regulate RNA metabolism and gene expression. RNA modifications, and the writers, erasers, and readers that catalyze these modifications, serve as important signaling machineries in cellular stress responses and disease pathogenesis. In response to stress, RNA modifications are mobilized to activate or inhibit the signaling pathways that combat stresses, including oxidative stress, hypoxia, therapeutic stress, metabolic stress, heat shock, DNA damage, and ER stress. The role of RNA modifications in response to these cellular stressors is context- and cell-type-dependent. Due to their pervasive roles in cell biology, RNA modifications have been implicated in the pathogenesis of different diseases, including cancer, neurologic and developmental disorders and diseases, and metabolic diseases. In this review, we aim to summarize the roles of RNA modifications in molecular and cellular stress responses and diseases.
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4
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Wang Q, Chen P, Liu J, Lou J, Liu Y, Yuan H. Xp11.22 duplications in four unrelated Chinese families: delineating the genotype-phenotype relationship for HSD17B10 and FGD1. BMC Med Genomics 2020; 13:66. [PMID: 32381089 PMCID: PMC7206777 DOI: 10.1186/s12920-020-0728-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 04/30/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Xp11.22 duplications have been reported to contribute to nonsyndromic intellectual disability (ID). The HUWE1 gene has been identified in all male Xp11.22 duplication patients and is associated with nonsyndromic ID. Currently, few Xp11.22 duplication cases have been reported in the Chinese population, with limited knowledge regarding the role of other genes in this interval. CASE PRESENTATION We investigated four unrelated Chinese male Xp11.22 duplication patients, performed a comprehensive clinical evaluation for the patients and discussed the role of other genes in this interval. All patients presented with similar clinical features, including ID, speech impairments and motor delay, which were mostly consistent with those of the Xp11.22 duplication described previously. We searched and compared all cases and noted that one of the probands (Family 1) and DECIPHER case 263,219, who carried small overlapping duplications at Xp11.22 that only covered the entire HSD17B10 gene, also suffered from ID, suggesting the important role of HSD17B10 in this interval. Furthermore, three patients (two probands in Families 3 and 4 and DECIPHER case 249,490) had strikingly similar hypogonadism phenotypes, including micropenis, small testes and cryptorchidism, which have not been previously described in Xp11.22 duplication patients. Interestingly, the FGD1 gene was duplicated only in these three patients. Sufficient evidence has suggested that haploinsufficiency of the FGD1 gene causes Aarskog-Scott syndrome, which is characterized by hypogonadism and other abnormalities. Given that, we are the first group to propose that FGD1 may be a potential dosage-sensitive gene responsible for the hypogonadism observed in our patients. CONCLUSION We reported novel genotypes and phenotypes in Chinese male Xp11.22 duplication patients, and the HSD17B10 and FGD1 genes may be involved.
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Affiliation(s)
- Qingming Wang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China
| | - Pengliang Chen
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Jianxin Liu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Jiwu Lou
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China
| | - Yanhui Liu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China.
| | - Haiming Yuan
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China.
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5
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Giles AC, Grill B. Roles of the HUWE1 ubiquitin ligase in nervous system development, function and disease. Neural Dev 2020; 15:6. [PMID: 32336296 PMCID: PMC7184716 DOI: 10.1186/s13064-020-00143-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Huwe1 is a highly conserved member of the HECT E3 ubiquitin ligase family. Here, we explore the growing importance of Huwe1 in nervous system development, function and disease. We discuss extensive progress made in deciphering how Huwe1 regulates neural progenitor proliferation and differentiation, cell migration, and axon development. We highlight recent evidence indicating that Huwe1 regulates inhibitory neurotransmission. In covering these topics, we focus on findings made using both vertebrate and invertebrate in vivo model systems. Finally, we discuss extensive human genetic studies that strongly implicate HUWE1 in intellectual disability, and heighten the importance of continuing to unravel how Huwe1 affects the nervous system.
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Affiliation(s)
- Andrew C Giles
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA
| | - Brock Grill
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA.
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6
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de Crécy-Lagard V, Boccaletto P, Mangleburg CG, Sharma P, Lowe TM, Leidel SA, Bujnicki JM. Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic Acids Res 2019; 47:2143-2159. [PMID: 30698754 PMCID: PMC6412123 DOI: 10.1093/nar/gkz011] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 12/25/2022] Open
Abstract
tRNA are post-transcriptionally modified by chemical modifications that affect all aspects of tRNA biology. An increasing number of mutations underlying human genetic diseases map to genes encoding for tRNA modification enzymes. However, our knowledge on human tRNA-modification genes remains fragmentary and the most comprehensive RNA modification database currently contains information on approximately 20% of human cytosolic tRNAs, primarily based on biochemical studies. Recent high-throughput methods such as DM-tRNA-seq now allow annotation of a majority of tRNAs for six specific base modifications. Furthermore, we identified large gaps in knowledge when we predicted all cytosolic and mitochondrial human tRNA modification genes. Only 48% of the candidate cytosolic tRNA modification enzymes have been experimentally validated in mammals (either directly or in a heterologous system). Approximately 23% of the modification genes (cytosolic and mitochondrial combined) remain unknown. We discuss these 'unidentified enzymes' cases in detail and propose candidates whenever possible. Finally, tissue-specific expression analysis shows that modification genes are highly expressed in proliferative tissues like testis and transformed cells, but scarcely in differentiated tissues, with the exception of the cerebellum. Our work provides a comprehensive up to date compilation of human tRNA modifications and their enzymes that can be used as a resource for further studies.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
- Cancer and Genetic Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
| | - Carl G Mangleburg
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Puneet Sharma
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
- Research Group for RNA Biochemistry, Institute of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznań, Poland
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7
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Evers C, Mitter D, Strobl-Wildemann G, Haug U, Hackmann K, Maas B, Janssen JWG, Jauch A, Hinderhofer K, Moog U. Duplication Xp11.22-p14 in females: does X-inactivation help in assessing their significance? Am J Med Genet A 2016; 167A:553-62. [PMID: 25691408 DOI: 10.1002/ajmg.a.36897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 10/31/2014] [Indexed: 11/08/2022]
Abstract
In females, large duplications in Xp often lead to preferential inactivation of the aberrant X chromosome and a normal phenotype. Recently, a recurrent ∼4.5 Mb microduplication of Xp11.22-p11.23 was found in females with developmental delay/intellectual disability and other neurodevelopmental disorders (speech development disorder, epilepsy or EEG anomalies, autism spectrum disorder, or behavioral disorder). Unexpectedly, most of them showed preferential inactivation of the normal X chromosome. We describe five female patients carrying de novo Xp duplications encompassing p11.23. Patient 1 carried the recurrent microduplication Xp11.22-p11.23, her phenotype and X-chromosome inactivation (XI) pattern was consistent with previous reports. The other four patients had novel Xp duplications. Two were monozygotic twins with a similar phenotype to Patient 1 and unfavorable XI skewing carrying an overlapping ∼5 Mb duplication of Xp11.23-p11.3. Patient 4 showed a duplication of ∼5.5 Mb comparable to the twins but had a more severe phenotype and unskewed XI. Patient 5 had a ∼8.5 Mb duplication Xp11.23-p11.4 and presented with mild ID, epilepsy, behavioral problems, and inconsistent results of XI analysis. A comparison of phenotype, size and location of the duplications and XI patterns in Patients 1-5 and previously reported females with overlapping duplications provides further evidence that microduplications encompassing Xp11.23 are associated with ID and other neurodevelopmental disorders in females. To further assess the implication of XI for female carriers, we recommend systematic analysis of XI pattern in any female with X imbalances that are known or suspected to be pathogenic.
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Affiliation(s)
- Christina Evers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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8
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Oikonomakis V, Kosma K, Mitrakos A, Sofocleous C, Pervanidou P, Syrmou A, Pampanos A, Psoni S, Fryssira H, Kanavakis E, Kitsiou-Tzeli S, Tzetis M. Recurrent copy number variations as risk factors for autism spectrum disorders: analysis of the clinical implications. Clin Genet 2016; 89:708-18. [PMID: 26777411 DOI: 10.1111/cge.12740] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 12/31/2022]
Abstract
Chromosomal microarray analysis (CMA) is currently considered a first-tier diagnostic assay for the investigation of autism spectrum disorders (ASD), developmental delay and intellectual disability of unknown etiology. High-resolution arrays were utilized for the identification of copy number variations (CNVs) in 195 ASD patients of Greek origin (126 males, 69 females). CMA resulted in the detection of 65 CNVs, excluding the known polymorphic copy number polymorphisms also found in the Database of Genomic Variants, for 51/195 patients (26.1%). Parental DNA testing in 20/51 patients revealed that 17 CNVs were de novo, 6 paternal and 3 of maternal origin. The majority of the 65 CNVs were deletions (66.1%), of which 5 on the X-chromosome while the duplications, of which 7 on the X-chromosome, were rarer (22/65, 33.8%). Fifty-one CNVs from a total of 65, reported for our cohort of ASD patients, were of diagnostic significance and well described in the literature while 14 CNVs (8 losses, 6 gains) were characterized as variants of unknown significance and need further investigation. Among the 51 patients, 39 carried one CNV, 10 carried two CNVs and 2 carried three CNVs. The use of CMA, its clinical validity and utility was assessed.
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Affiliation(s)
- V Oikonomakis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - K Kosma
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Mitrakos
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - C Sofocleous
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Research Institute for the Study of Genetic and Malignant Diseases in Childhood, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - P Pervanidou
- 1st Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Syrmou
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Pampanos
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Department of Genetics, "Alexandra" University Maternal Hospital, Athens, Greece
| | - S Psoni
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - H Fryssira
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - E Kanavakis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.,Research Institute for the Study of Genetic and Malignant Diseases in Childhood, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - S Kitsiou-Tzeli
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Tzetis
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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9
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Landmarks in the Evolution of (t)-RNAs from the Origin of Life up to Their Present Role in Human Cognition. Life (Basel) 2015; 6:life6010001. [PMID: 26703740 PMCID: PMC4810232 DOI: 10.3390/life6010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
How could modern life have evolved? The answer to that question still remains unclear. However, evidence is growing that, since the origin of life, RNA could have played an important role throughout evolution, right up to the development of complex organisms and even highly sophisticated features such as human cognition. RNA mediated RNA-aminoacylation can be seen as a first landmark on the path from the RNA world to modern DNA- and protein-based life. Likewise, the generation of the RNA modifications that can be found in various RNA species today may already have started in the RNA world, where such modifications most likely entailed functional advantages. This association of modification patterns with functional features was apparently maintained throughout the further course of evolution, and particularly tRNAs can now be seen as paradigms for the developing interdependence between structure, modification and function. It is in this spirit that this review highlights important stepping stones of the development of (t)RNAs and their modifications (including aminoacylation) from the ancient RNA world up until their present role in the development and maintenance of human cognition. The latter can be seen as a high point of evolution at its present stage, and the susceptibility of cognitive features to even small alterations in the proper structure and functioning of tRNAs underscores the evolutionary relevance of this RNA species.
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10
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Grams SE, Argiropoulos B, Lines M, Chakraborty P, Mcgowan-Jordan J, Geraghty MT, Tsang M, Eswara M, Tezcan K, Adams KL, Linck L, Himes P, Kostiner D, Zand DJ, Stalker H, Driscoll DJ, Huang T, Rosenfeld JA, Li X, Chen E. Genotype-phenotype characterization in 13 individuals with chromosome Xp11.22 duplications. Am J Med Genet A 2015; 170A:967-77. [PMID: 26692240 DOI: 10.1002/ajmg.a.37519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/25/2015] [Indexed: 11/10/2022]
Abstract
We report 13 new individuals with duplications in Xp11.22-p11.23. The index family has one male and two female members in three generations with mild-severe intellectual disability (ID), speech delay, dysmorphic features, early puberty, constipation, and/or hand and foot abnormalities. Affected individuals were found to have two small duplications in Xp11.22 at nucleotide position (hg19) 50,112,063-50,456,458 bp (distal) and 53,160,114-53,713,154 bp (proximal). Collectively, these two regions include 14 RefSeq genes, prompting collection of a larger cohort of patients, in an attempt to delineate critical genes associated with the observed phenotype. In total, we have collected data on nine individuals with duplications overlapping the distal duplication region containing SHROOM4 and DGKK and eight individuals overlapping the proximal region including HUWE1. Duplications of HUWE1 have been previously associated with non-syndromic ID. Our data, with previously published reports, suggest that duplications involving SHROOM4 and DGKK may represent a new syndromic X-linked ID critical region associated with mild to severe ID, speech delay +/- dysarthria, attention deficit disorder, precocious puberty, constipation, and motor delay. We frequently observed foot abnormalities, 5th finger clinodactyly, tapering fingers, constipation, and exercise intolerance in patients with duplications of these two genes. Regarding duplications including the proximal region, our observations agree with previous studies, which have found associations with intellectual disability. In addition, expressive language delay, failure to thrive, motor delay, and 5th finger clinodactyly were also frequently observed in patients with the proximal duplication.
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Affiliation(s)
- Sarah E Grams
- Department of Medical Genetics, Kaiser Permanente, San Francisco, California
| | - Bob Argiropoulos
- Alberta Children's Hospital Research Institute for Child and Maternal Health, Alberta, Canada
| | - Matthew Lines
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Pranesh Chakraborty
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean Mcgowan-Jordan
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Michael T Geraghty
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Marilyn Tsang
- Department of Genetics, Sutter Memorial Hospital, Sacramento, California
| | - Marthand Eswara
- Department of Genetics, Sutter Memorial Hospital, Sacramento, California
| | - Kamer Tezcan
- Department of Genetics, Kaiser Permanente, Sacramento, California
| | - Kelly L Adams
- Department of Genetics, Kaiser Permanente, Sacramento, California
| | - Leesa Linck
- Department of Medical Genetics, Kaiser Permanente, Portland, Oregon
| | - Patricia Himes
- Department of Medical Genetics, Kaiser Permanente, Portland, Oregon
| | - Dana Kostiner
- Department of Medical Genetics, Kaiser Permanente, Portland, Oregon
| | - Dina J Zand
- Department of Medical Genetics, Children's National Medical Center, Washington DC
| | - Heather Stalker
- Department of Genetics, University of Florida, Gainesville, Florida
| | | | - Taosheng Huang
- Department of Human Genetics, Children's Hospital of Orange County, Orange, California
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, Perkin Elmer, Inc., Spokane, Washington
| | - Xu Li
- Department of Genetics, Kaiser Permanente, San Jose, California
| | - Emily Chen
- Department of Medical Genetics, Kaiser Permanente, San Francisco, California.,Department of Genetics, Kaiser Permanente, San Jose, California
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11
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Nizon M, Andrieux J, Rooryck C, de Blois MC, Bourel-Ponchel E, Bourgois B, Boute O, David A, Delobel B, Duban-Bedu B, Giuliano F, Goldenberg A, Grotto S, Héron D, Karmous-Benailly H, Keren B, Lacombe D, Lapierre JM, Le Caignec C, Le Galloudec E, Le Merrer M, Le Moing AG, Mathieu-Dramard M, Nusbaum S, Pichon O, Pinson L, Raoul O, Rio M, Romana S, Roubertie A, Colleaux L, Turleau C, Vekemans M, Nabbout R, Malan V. Phenotype-genotype correlations in 17 new patients with an Xp11.23p11.22 microduplication and review of the literature. Am J Med Genet A 2014; 167A:111-22. [PMID: 25425167 DOI: 10.1002/ajmg.a.36807] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 09/04/2014] [Indexed: 11/12/2022]
Abstract
Array comparative genomic hybridization (array CGH) has proven its utility in uncovering cryptic rearrangements in patients with X-linked intellectual disability. In 2009, Giorda et al. identified inherited and de novo recurrent Xp11.23p11.22 microduplications in two males and six females from a wide cohort of patients presenting with syndromic intellectual disability. To date, 14 females and 5 males with an overlapping microduplication have been reported in the literature. To further characterize this emerging syndrome, we collected clinical and microarray data from 17 new patients, 10 females, and 7 males. The Xp11.23p11.2 microduplications detected by array CGH ranged in size from 331 Kb to 8.9 Mb. Five patients harbored 4.5 Mb recurrent duplications mediated by non-allelic homologous recombination between segmental duplications and 12 harbored atypical duplications. The chromosomal rearrangement occurred de novo in eight patients and was inherited in six affected males from three families. Patients shared several common major characteristics including moderate to severe intellectual disability, early onset of puberty, language impairment, and age related epileptic syndromes such as West syndrome and focal epilepsy with activation during sleep evolving in some patients to continuous spikes-and-waves during slow sleep. Atypical microduplications allowed us to identify minimal critical regions that might be responsible for specific clinical findings of the syndrome and to suggest possible candidate genes: FTSJ1 and SHROOM4 for intellectual disability along with PQBP1 and SLC35A2 for epilepsy. Xp11.23p11.22 microduplication is a recently-recognized syndrome associated with intellectual disability, epilepsy, and early onset of puberty in females. In this study, we propose several genes that could contribute to the phenotype.
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Affiliation(s)
- Mathilde Nizon
- Département de Génétique, Université Paris Descartes, Sorbonne Paris Cité, Institut IMAGINE UMR_S1163, Hôpital Necker-Enfants Malades, Paris, France
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12
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Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends Mol Med 2014; 20:306-14. [PMID: 24581449 DOI: 10.1016/j.molmed.2014.01.008] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/17/2014] [Accepted: 01/23/2014] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are key for efficient and accurate protein translation. To be fully active, tRNAs need to be heavily modified post-transcriptionally. Growing evidence indicates that tRNA modifications and the enzymes catalyzing such modifications may play important roles in complex human pathologies. Here, we have compiled current knowledge that directly link tRNA modifications to human diseases such as cancer, type 2 diabetes (T2D), neurological disorders, and mitochondrial-linked disorders. The molecular mechanisms behind these connections remain, for the most part, unknown. As we progress towards the understanding of the roles played by hypomodified tRNAs in human disease, novel areas of therapeutic intervention may be discovered.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010 Catalunya, Spain
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010 Catalunya, Spain.
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13
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Sarin LP, Leidel SA. Modify or die?--RNA modification defects in metazoans. RNA Biol 2014; 11:1555-67. [PMID: 25692999 PMCID: PMC4615230 DOI: 10.4161/15476286.2014.992279] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 12/21/2022] Open
Abstract
Chemical RNA modifications are present in all kingdoms of life and many of these post-transcriptional modifications are conserved throughout evolution. However, most of the research has been performed on single cell organisms, whereas little is known about how RNA modifications contribute to the development of metazoans. In recent years, the identification of RNA modification genes in genome wide association studies (GWAS) has sparked new interest in previously neglected genes. In this review, we summarize recent findings that connect RNA modification defects and phenotypes in higher eukaryotes. Furthermore, we discuss the implications of aberrant tRNA modification in various human diseases including metabolic defects, mitochondrial dysfunctions, neurological disorders, and cancer. As the molecular mechanisms of these diseases are being elucidated, we will gain first insights into the functions of RNA modifications in higher eukaryotes and finally understand their roles during development.
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MESH Headings
- Amyotrophic Lateral Sclerosis/genetics
- Amyotrophic Lateral Sclerosis/metabolism
- Amyotrophic Lateral Sclerosis/pathology
- Animals
- Dysautonomia, Familial/genetics
- Dysautonomia, Familial/metabolism
- Dysautonomia, Familial/pathology
- Epilepsy, Rolandic/genetics
- Epilepsy, Rolandic/metabolism
- Epilepsy, Rolandic/pathology
- Genome-Wide Association Study
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Mutation
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Nucleic Acid Conformation
- Phenotype
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- L Peter Sarin
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
- Faculty of Medicine; University of Münster; Münster, Germany
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14
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Froyen G, Belet S, Martinez F, Santos-Rebouças C, Declercq M, Verbeeck J, Donckers L, Berland S, Mayo S, Rosello M, Pimentel M, Fintelman-Rodrigues N, Hovland R, Rodrigues dos Santos S, Raymond F, Bose T, Corbett M, Sheffield L, van Ravenswaaij-Arts C, Dijkhuizen T, Coutton C, Satre V, Siu V, Marynen P. Copy-number gains of HUWE1 due to replication- and recombination-based rearrangements. Am J Hum Genet 2012; 91:252-64. [PMID: 22840365 DOI: 10.1016/j.ajhg.2012.06.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/21/2012] [Accepted: 06/21/2012] [Indexed: 12/20/2022] Open
Abstract
We previously reported on nonrecurrent overlapping duplications at Xp11.22 in individuals with nonsyndromic intellectual disability (ID) harboring HSD17B10, HUWE1, and the microRNAs miR-98 and let-7f-2 in the smallest region of overlap. Here, we describe six additional individuals with nonsyndromic ID and overlapping microduplications that segregate in the families. High-resolution mapping of the 12 copy-number gains reduced the minimal duplicated region to the HUWE1 locus only. Consequently, increased mRNA levels were detected for HUWE1, but not HSD17B10. Marker and SNP analysis, together with identification of two de novo events, suggested a paternally derived intrachromosomal duplication event. In four independent families, we report on a polymorphic 70 kb recurrent copy-number gain, which harbors part of HUWE1 (exon 28 to 3' untranslated region), including miR-98 and let-7f-2. Our findings thus demonstrate that HUWE1 is the only remaining dosage-sensitive gene associated with the ID phenotype. Junction and in silico analysis of breakpoint regions demonstrated simple microhomology-mediated rearrangements suggestive of replication-based duplication events. Intriguingly, in a single family, the duplication was generated through nonallelic homologous recombination (NAHR) with the use of HUWE1-flanking imperfect low-copy repeats, which drive this infrequent NAHR event. The recurrent partial HUWE1 copy-number gain was also generated through NAHR, but here, the homologous sequences used were identified as TcMAR-Tigger DNA elements, a template that has not yet been reported for NAHR. In summary, we showed that an increased dosage of HUWE1 causes nonsyndromic ID and demonstrated that the Xp11.22 region is prone to recombination- and replication-based rearrangements.
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15
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Dombret C, Nguyen T, Schakman O, Michaud JL, Hardin-Pouzet H, Bertrand MJ, De Backer O. Loss of Maged1 results in obesity, deficits of social interactions, impaired sexual behavior and severe alteration of mature oxytocin production in the hypothalamus. Hum Mol Genet 2012; 21:4703-17. [DOI: 10.1093/hmg/dds310] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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16
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Becker KG. Male gender bias in autism and pediatric autoimmunity. Autism Res 2012; 5:77-83. [PMID: 22431266 PMCID: PMC4530611 DOI: 10.1002/aur.1227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 01/23/2012] [Indexed: 12/13/2022]
Abstract
Male bias in both autism and pediatric autoimmune disease is thought to involve hormonal perturbations in pregnancy or early childhood in the context of genetic control. These early molecular events, at a time of rapid development, are intimately linked to concurrent development in the brain and immune system. It is suggested here that these early regulatory events may overlap between autism and autoimmunity in determining male sex bias and may provide evidence of an etiological link among autism, immune dysregulation, and autoimmune disease.
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Affiliation(s)
- Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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17
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El-Hattab AW, Bournat J, Eng PA, Wu JBS, Walker BA, Stankiewicz P, Cheung SW, Brown CW. Microduplication of Xp11.23p11.3 with effects on cognition, behavior, and craniofacial development. Clin Genet 2011; 79:531-8. [PMID: 20662849 DOI: 10.1111/j.1399-0004.2010.01496.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report an ~1.3 Mb tandem duplication at Xp11.23p11.3 in an 11-year-old boy with pleasant personality, hyperactivity, learning and visual-spatial difficulties, relative microcephaly, long face, stellate iris pattern, and periorbital fullness. This clinical presentation is milder and distinct from that of patients with partially overlapping Xp11.22p11.23 duplications which have been described in males and females with intellectual disability, language delay, autistic behaviors, and seizures. The duplicated region harbors three known X-linked mental retardation genes: FTSJ1, ZNF81, and SYN1. Quantitative polymerase chain reaction from whole blood total RNA showed increased expression of three genes located in the duplicated region: EBP, WDR13, and ZNF81. Thus, over-expression of genes in the interval may contribute to the observed phenotype. Many of the features seen in this patient are present in individuals with Williams-Beuren syndrome (WBS). Interestingly, the SYN1 gene within the duplicated interval, as well as the STX1A gene, within the WBS critical region, co-localize to presynaptic active zones, and play important roles in neurotransmitter release.
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Affiliation(s)
- A W El-Hattab
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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18
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Chung BHY, Drmic I, Marshall CR, Grafodatskaya D, Carter M, Fernandez BA, Weksberg R, Roberts W, Scherer SW. Phenotypic spectrum associated with duplication of Xp11.22-p11.23 includes Autism Spectrum Disorder. Eur J Med Genet 2011; 54:e516-20. [PMID: 21689796 DOI: 10.1016/j.ejmg.2011.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 05/26/2011] [Indexed: 12/13/2022]
Abstract
Dup(X)(p11.22-p11.23) has been shown to be associated with intellectual disability (ID, also referred to as mental retardation). Here, we characterize a 4.64 Mb de novo duplication of the same Xp11.22-p11.23 ID region in a female, but for this reference case the diagnosis was Autism Spectrum Disorder (ASD). Besides ASD, she also had very persistent trichotillomania, anxiety symptoms and some non-specific dysmorphic features. We report the detailed clinical features, as well as refine the rearrangement breakpoints of this disease-associated copy number variation region, which encompasses more than 50 genes. We propose that in addition to ID, the phenotypic spectrum associated with dup(X)(p11.22-p11.23) can include ASD, language impairment, and/or other primary psychiatric disorders.
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Affiliation(s)
- Brian H Y Chung
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
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19
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Whole gene duplication of the PQBP1 gene in syndrome resembling Renpenning. Am J Med Genet A 2010; 155A:141-4. [DOI: 10.1002/ajmg.a.33756] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Accepted: 09/06/2010] [Indexed: 11/07/2022]
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20
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Siggberg L, Ala-Mello S, Jaakkola E, Kuusinen E, Schuit R, Kohlhase J, Böhm D, Ignatius J, Knuutila S. Array CGH in molecular diagnosis of mental retardation - A study of 150 Finnish patients. Am J Med Genet A 2010; 152A:1398-410. [PMID: 20503314 DOI: 10.1002/ajmg.a.33402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report on the results of an array comparative genomic hybridization (array CGH) study of 150 karyotypically normal Finnish patients with idiopathic mental retardation and/or dysmorphic features and/or malformations. Using high-resolution microarray analysis, we sought to identify clinically relevant microdeletions and microduplications in these patients. The results were confirmed using other methods and compared with findings reported in recent publications and internet databases. Small aberrations of potential clinical significance were found in 28 (18.6%) of the 150 patients. Eight of the identified aberrations are known to cause syndromes, 4 affected the X chromosome in males, 4 were familial, and 13 have yet to be associated with a phenotype. This study demonstrates the benefits of array CGH in clinical diagnostics of developmental disorders. Further, our findings give evidence of new syndromes.
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Affiliation(s)
- Linda Siggberg
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland.
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21
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Zou YS, Milunsky JM. Developmental disability and hypomelanosis of Ito in a female with 7.3 Mb de novo duplication of Xp11.3-p11.4 and random X inactivation. Am J Med Genet A 2010; 149A:2573-7. [PMID: 19876908 DOI: 10.1002/ajmg.a.33066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ying S Zou
- Center for Human Genetics, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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22
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Complex segmental duplications mediate a recurrent dup(X)(p11.22-p11.23) associated with mental retardation, speech delay, and EEG anomalies in males and females. Am J Hum Genet 2009; 85:394-400. [PMID: 19716111 DOI: 10.1016/j.ajhg.2009.08.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 07/31/2009] [Accepted: 08/05/2009] [Indexed: 11/22/2022] Open
Abstract
Submicroscopic copy-number variations make a considerable contribution to the genetic etiology of human disease. We have analyzed subjects with idiopathic mental retardation (MR) by using whole-genome oligonucleotide-based array comparative genomic hybridization (aCGH) and identified familial and de novo recurrent Xp11.22-p11.23 duplications in males and females with MR, speech delay, and a peculiar electroencephalographic (EEG) pattern in childhood. The size of the duplications ranges from 0.8-9.2 Mb. Most affected females show preferential activation of the duplicated X chromosome. Carriers of the smallest duplication show X-linked recessive inheritance. All other affected individuals present dominant expression and comparable clinical phenotypes irrespective of sex, duplication size, and X-inactivation pattern. The majority of the rearrangements are mediated by recombination between flanking complex segmental duplications. The identification of common clinical features, including the typical EEG pattern, predisposing genomic structure, and peculiar X-inactivation pattern, suggests that duplication of Xp11.22-p11.23 constitutes a previously undescribed syndrome.
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23
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Hunter M, Bruno D, Amor DJ. Functional disomy of proximal Xp causes a distinct phenotype comprising early hypotonia, hypertelorism, small hands and feet, ear abnormalities, myopia and cognitive impairment. Am J Med Genet A 2009; 149A:1763-7. [DOI: 10.1002/ajmg.a.32954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Gong P, Li J, Dai L, Zhang K, Zheng Z, Gao X, Zhang F. Genetic variations in FTSJ1 influence cognitive ability in young males in the Chinese Han population. J Neurogenet 2009; 22:277-87. [PMID: 19012053 DOI: 10.1080/01677060802337299] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Human cognitive ability is a trait that is known to be significantly influenced by genetic factors. Previous linkage data provide evidence suggesting that gene FtsJ homolog 1 (Escherichia coli) is associated with mental retardation. The gene may have a relation to individual differences in cognitive ability because it is most critical for brain development. In the present research, three tag single-nucleotide polymorphism (SNPs) (rs2268954, rs2070991, and rs5905692) in FtsJ homolog 1 (E. coli) are selected and genotyped by the PCR-SSCP method. An analysis of variance is performed to determine the relationship between the SNPs and cognitive ability of the Chinese Han population of youth in Qinba mountain. There are significant correlations between the variance in FtsJ homolog 1 (E. coli) and general cognitive ability, verbal comprehension, and preceptual organization. These findings suggest that genetic variations in FtsJ homolog 1 (E. coli) possibly influence human cognitive ability.
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Affiliation(s)
- Pingyuan Gong
- School of Life Science, Institute of Population and Health, Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, China
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25
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Christian SL, Brune CW, Sudi J, Kumar RA, Liu S, Karamohamed S, Badner JA, Matsui S, Conroy J, McQuaid D, Gergel J, Hatchwell E, Gilliam TC, Gershon ES, Nowak NJ, Dobyns WB, Cook EH. Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder. Biol Psychiatry 2008; 63:1111-7. [PMID: 18374305 PMCID: PMC2440346 DOI: 10.1016/j.biopsych.2008.01.009] [Citation(s) in RCA: 213] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 01/10/2008] [Accepted: 01/22/2008] [Indexed: 11/24/2022]
Abstract
BACKGROUND One genetic mechanism known to be associated with autism spectrum disorders (ASD) is chromosomal abnormalities. The identification of copy number variants (CNV), i.e., microdeletions and microduplications that are undetectable at the level of traditional cytogenetic analysis, allows the potential association of submicroscopic chromosomal imbalances and human disease. METHODS We performed array comparative genomic hybridization (aCGH) utilizing a 19K whole genome tiling path bacterial artificial chromosome (BAC) microarray on 397 unrelated subjects with autism spectrum disorder. Common CNV were excluded using a control group comprised of 372 individuals from the National Institute of Mental Health (NIMH) Genetics Initiative Control samples. Confirmation studies were performed on all remaining CNV using fluorescence in situ hybridization (FISH), microsatellite analysis, and/or quantitative polymerase chain reaction (PCR) analysis. RESULTS A total of 51 CNV were confirmed in 46 ASD subjects. Three maternal interstitial duplications of 15q11-q13 known to be associated with ASD were identified. The other 48 CNV ranged in size from 189 kilobase (kb) to 5.5 megabase (Mb) and contained from 0 to approximately 40 National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) genes. Seven CNV were de novo and 44 were inherited. CONCLUSIONS Fifty-one autism-specific CNV were identified in 46 of 397 ASD patients using a 19K BAC microarray for an overall rate of 11.6%. These microdeletions and microduplications cause gene dosage imbalance in 272 genes, many of which could be considered as candidate genes for autism.
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Affiliation(s)
- Susan L Christian
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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26
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Monnot S, Giuliano F, Massol C, Fossoud C, Cossée M, Lambert JC, Karmous-Benailly H. Partial Xp11.23-p11.4 duplication with random X inactivation: clinical report and molecular cytogenetic characterization. Am J Med Genet A 2008; 146A:1325-9. [PMID: 18412111 DOI: 10.1002/ajmg.a.32238] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Partial duplications of the short arm of the X chromosome are relatively rare and have been described in males and females. We describe a 4 10/12-year-old girl presenting with developmental delay, severe language retardation and minor anomalies with slightly elevated head circumference (+1.8 SD), prominent forehead, wide palpebral fissures and anteverted nares. No pigmentary dysplasia of the skin was present. The external genitalia were normal. The karyotype completed by cytogenetic analysis with the Whole Chromosome Painting probe of chromosome X revealed a de novo partial duplication of the short arm of an X chromosome. In order to further characterize the duplicated segment, we used a series of BAC probes extending from band Xp11.22 to Xp22.1. BACs from Xp11.23 to Xp11.4 were duplicated. The karyotype was finally defined as 46,X,dup(X)(p11p11).ish dup(X)(p11.23p11.4)(WCPX+,RP11-416I6++,RP11-386N14++,RP11-466C12++). The X-inactivation status was studied using the human androgen receptor (HUMARA) and the FRAXA locus methylation assay. Unexpectedly, the two X chromosomes were found to be randomly inactivated, in the proband. Indeed, usually, in women with structurally abnormal X chromosome, the abnormal X chromosome is preferentially inactivated and those patients share an apparent normal phenotype. So, we speculate that in the present case, the phenotype of the patient could be explained by a functional disomy of the genes present in the duplicated region. We will discuss the possible implication of these genes on the observed phenotype.
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Affiliation(s)
- Sophie Monnot
- Department of Medical Genetics, Hospital Archet 2, CHU Nice, France.
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27
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Qiao Y, Liu X, Harvard C, Hildebrand MJ, Rajcan-Separovic E, Holden JJA, Lewis MES. Autism-associated familial microdeletion of Xp11.22. Clin Genet 2008; 74:134-44. [PMID: 18498374 DOI: 10.1111/j.1399-0004.2008.01028.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe two brothers with autistic disorder, intellectual disability (ID) and cleft lip/palate with a microdeletion of Xp11.22 detected through screening individuals with autism spectrum disorders (ASDs) for microdeletions and duplications using 1-Mb resolution array comparative genomic hybridization. The deletion was confirmed by fluorescence in situ hybridization/real-time quantitative polymerase chain reaction (RT-qPCR) and shown to be inherited from their unaffected mother who had skewed (100%) X inactivation of the aberrant chromosome. RT-qPCR characterization of the del(X)(p11.22) region ( approximately 53,887,000-54,359,000 bp) revealed complete deletion of the plant homeodomain finger protein 8 (PHF8) gene as well as deletions of the FAM120C and WNK lysine-deficient protein kinase 3 (WNK3) genes, for which a definitive phenotype has not been previously characterized. Xp11.2 is a gene-rich region within the critical linkage interval for several neurodevelopmental disorders. Rare interstitial microdeletions of Xp11.22 have been recognized with ID, craniofacial dysmorphism and/or cleft lip/palate and truncating mutations of the PHF8 gene within this region. Despite evidence implicating genes within Xp11.22 with language and cognitive development that could contribute to an ASD phenotype, their involvement with autism has not been systematically evaluated. Population screening of 481 (319 males/81 females) and 282 X chromosomes (90 males/96 females) in respective ASD and control cohorts did not identify additional subjects carrying this deletion. Our findings show that in addition to point mutations, a complete deletion of the PHF8 gene is associated with the X-linked mental retardation Siderius-Hamel syndrome (OMIM 300263) and further suggest that the larger size of the Xp11.22 deletion including genes FAM120C and WNK3 may be involved in the pathogenesis of autism.
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Affiliation(s)
- Y Qiao
- Department of Medical Genetics, and Department of Pathology, Child and Family Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
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28
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Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, Thiruvahindrapduram B, Fiebig A, Schreiber S, Friedman J, Ketelaars CEJ, Vos YJ, Ficicioglu C, Kirkpatrick S, Nicolson R, Sloman L, Summers A, Gibbons CA, Teebi A, Chitayat D, Weksberg R, Thompson A, Vardy C, Crosbie V, Luscombe S, Baatjes R, Zwaigenbaum L, Roberts W, Fernandez B, Szatmari P, Scherer SW. Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 2008; 82:477-88. [PMID: 18252227 DOI: 10.1016/j.ajhg.2007.12.009] [Citation(s) in RCA: 1300] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 12/18/2007] [Accepted: 12/19/2007] [Indexed: 02/03/2023] Open
Abstract
Structural variation (copy number variation [CNV] including deletion and duplication, translocation, inversion) of chromosomes has been identified in some individuals with autism spectrum disorder (ASD), but the full etiologic role is unknown. We performed genome-wide assessment for structural abnormalities in 427 unrelated ASD cases via single-nucleotide polymorphism microarrays and karyotyping. With microarrays, we discovered 277 unbalanced CNVs in 44% of ASD families not present in 500 controls (and re-examined in another 1152 controls). Karyotyping detected additional balanced changes. Although most variants were inherited, we found a total of 27 cases with de novo alterations, and in three (11%) of these individuals, two or more new variants were observed. De novo CNVs were found in approximately 7% and approximately 2% of idiopathic families having one child, or two or more ASD siblings, respectively. We also detected 13 loci with recurrent/overlapping CNV in unrelated cases, and at these sites, deletions and duplications affecting the same gene(s) in different individuals and sometimes in asymptomatic carriers were also found. Notwithstanding complexities, our results further implicate the SHANK3-NLGN4-NRXN1 postsynaptic density genes and also identify novel loci at DPP6-DPP10-PCDH9 (synapse complex), ANKRD11, DPYD, PTCHD1, 15q24, among others, for a role in ASD susceptibility. Our most compelling result discovered CNV at 16p11.2 (p = 0.002) (with characteristics of a genomic disorder) at approximately 1% frequency. Some of the ASD regions were also common to mental retardation loci. Structural variants were found in sufficiently high frequency influencing ASD to suggest that cytogenetic and microarray analyses be considered in routine clinical workup.
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Affiliation(s)
- Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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29
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Lugtenberg D, Veltman JA, van Bokhoven H. High-resolution genomic microarrays for X-linked mental retardation. Genet Med 2007; 9:560-5. [PMID: 17873643 DOI: 10.1097/gim.0b013e318149e647] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Developments in genomic microarray technology have revolutionized the study of human genomic copy number variation. This has significantly affected many areas in human genetics, including the field of X-linked mental retardation (XLMR). Chromosome X-specific bacterial artificial chromosomes microarrays have been developed to specifically test this chromosome with a resolution of approximately 100 kilobases. Application of these microarrays in X-linked mental retardation studies has resulted in the identification of novel X-linked mental retardation genes, copy number variation at known X-linked mental retardation genes, and copy number variations harboring as yet unidentified X-linked mental retardation genes. Further enhancements in genomic microarray analysis will soon allow the reliable analysis of all copy number variations throughout this chromosome at the kilobase or single exon resolution. In this review, we describe the developments in this field and specifically highlight the impact of these microarray studies in the field of X-linked mental retardation.
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Affiliation(s)
- Dorien Lugtenberg
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Tabor HK, Cho MK. Ethical implications of array comparative genomic hybridization in complex phenotypes: points to consider in research. Genet Med 2007; 9:626-31. [PMID: 17873651 PMCID: PMC2220022 DOI: 10.1097/gim.0b013e3181485688] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
As with many new diagnostic technologies, the recent rapid emergence of array comparative genome hybridization in clinical genetics provides the power to observe new biological phenomena before their clinical significance is well understood. This raises ethical issues for clinicians when applying the technologies. However, at this early stage of research and development on array comparative genome hybridization, the ethical implications of the conduct of research, as well as how research findings are presented and interpreted, should also be considered by the research, clinical, and ethics communities. These considerations are especially important in the use of array comparative genome hybridization to study complex and common traits. We examined recent publications on autism as an example of the application of array comparative genome hybridization to a complex phenotype. Our goal was to identify points to consider for researchers, clinicians, and patients/families to ensure responsible and ethical design, presentation, and interpretation of these kinds of studies.
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Affiliation(s)
- Holly K Tabor
- Stanford Center for Biomedical Ethics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California, USA.
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Froyen G, Bauters M, Boyle J, Van Esch H, Govaerts K, van Bokhoven H, Ropers HH, Moraine C, Chelly J, Fryns JP, Marynen P, Gecz J, Turner G. Loss of SLC38A5 and FTSJ1 at Xp11.23 in three brothers with non-syndromic mental retardation due to a microdeletion in an unstable genomic region. Hum Genet 2007; 121:539-47. [PMID: 17333282 DOI: 10.1007/s00439-007-0343-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 02/07/2007] [Indexed: 12/26/2022]
Abstract
Using high resolution X chromosome array-CGH we identified an interstitial microdeletion at Xp11.23 in three brothers with moderate to severe mental retardation (MR) without dysmorphic features. The extent of the deletion was subsequently delineated to about 50 kb by regular PCR and included only the SLC38A5 and FTSJ1 genes. The loss of the FTSJ1 MR gene in males is expected to result in the observed phenotype but the contribution of the deletion of the solute carrier SLC38A5 gene is less clear. Their mother also carries the deletion and completely inactivates the aberrant X chromosome. Interestingly, the distal breakpoint is situated within a 200 kb SSX repeat region that appears to stimulate recombination since subtle copy number changes often occur at this location and it is frequently involved in translocations in tumours. Since this apparent SSX unstable structure is flanked proximally by FTSJ1 and PQBP1, subtle deletions or duplications at this location would be expected to cause MR, as in our family. So far, we have screened a cohort of 300 patients but did not find additional aberrations at the FTSJ1 locus indicating that the frequency is likely to be low.
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Affiliation(s)
- Guy Froyen
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB, Leuven, Belgium.
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