1
|
Biswal SR, Kumar A, Muthuswamy S, Kumar S. Genetic components of microdeletion syndromes and their role in determining schizophrenia traits. Mol Biol Rep 2024; 51:804. [PMID: 39001960 DOI: 10.1007/s11033-024-09731-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/17/2024] [Indexed: 07/15/2024]
Abstract
Schizophrenia is a neuropsychiatric disorder characterized by various symptoms such as hallucinations, delusions, and disordered thinking. The etiology of this disease is unknown; however, it has been linked to many microdeletion syndromes that are likely to contribute to the pathology of schizophrenia. In this review we have comprehensively analyzed the role of various microdeletion syndromes, like 3q29, 15q13.3, and 22q11.2, which are known to be involved with schizophrenia. A variety of factors lead to schizophrenia phenotypes, but copy number variants that disrupt gene regulation and impair brain function and cognition are one of the causes that have been identified. Multiple case studies have shown that loss of one or more genes in the microdeletion regions lead to brain activity defects. In this article, we present a coherent paradigm that connects copy number variations (CNVs) to numerous neurological and behavioral abnormalities associated with schizophrenia. It would be helpful in understanding the different aspects of the microdeletions and how they contribute in the pathophysiology of schizophrenia.
Collapse
Affiliation(s)
- Smruti Rekha Biswal
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India
| | - Ajay Kumar
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Srinivasan Muthuswamy
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India.
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India.
| |
Collapse
|
2
|
A unique Smith-Magenis patient with a de novo intragenic deletion on the maternally inherited overexpressed RAI1 allele. Eur J Hum Genet 2022; 30:1233-1238. [PMID: 35821519 PMCID: PMC9626456 DOI: 10.1038/s41431-022-01143-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/01/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
RAI1 is a dosage-sensitive gene whose decreased or increased expression by recurrent and non-recurrent 17p11.2 deletions or duplications causes Smith-Magenis (SMS) or Potocki-Lupski syndromes (PTLS), respectively. Here we report on a 21-year-old female patient showing SMS phenotype who was found to carry a 3.4 kb de novo intragenic RAI1 deletion. Interestingly, a significant increase in RAI1 transcript levels was identified in the patient's, brother's and mother's peripheral blood cells. Allele-specific dosage analysis revealed that the patient's maternally inherited overexpressed RAI1 allele harbors the intragenic deletion, confirming the SMS diagnosis due to the presence of a single wild-type RAI1 functional allele. The mother and brother do not present any PTLS neurologic/behavioral clinical features. Extensive sequencing of RAI1 promoter and predicted regulatory regions showed no potential causative variants accounting for gene overexpression. However, the mother and both children share a novel private missense variant in RAI1 exon 3, currently classified as a VUS (uncertain significance), though predicted by two bioinformatic tools to disrupt the binding site of one specific transcription factor. The reported familial case, the second showing RAI1 overexpression in the absence of RAI1 duplication, may help to understand the regulation of RAI1 dosage sensitivity although its phenotypic effect remains to be determined.
Collapse
|
3
|
Lupski JR. Clan genomics: From OMIM phenotypic traits to genes and biology. Am J Med Genet A 2021; 185:3294-3313. [PMID: 34405553 PMCID: PMC8530976 DOI: 10.1002/ajmg.a.62434] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
Collapse
Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| |
Collapse
|
4
|
Woo EG, Tayebi N, Sidransky E. Next-Generation Sequencing Analysis of GBA1: The Challenge of Detecting Complex Recombinant Alleles. Front Genet 2021; 12:684067. [PMID: 34234814 PMCID: PMC8255797 DOI: 10.3389/fgene.2021.684067] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/27/2021] [Indexed: 01/23/2023] Open
Affiliation(s)
- Elizabeth G Woo
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
5
|
Faoro C, Ataide SF. Noncanonical Functions and Cellular Dynamics of the Mammalian Signal Recognition Particle Components. Front Mol Biosci 2021; 8:679584. [PMID: 34113652 PMCID: PMC8185352 DOI: 10.3389/fmolb.2021.679584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/29/2021] [Indexed: 12/24/2022] Open
Abstract
The signal recognition particle (SRP) is a ribonucleoprotein complex fundamental for co-translational delivery of proteins to their proper membrane localization and secretory pathways. Literature of the past two decades has suggested new roles for individual SRP components, 7SL RNA and proteins SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72, outside the SRP cycle. These noncanonical functions interconnect SRP with a multitude of cellular and molecular pathways, including virus-host interactions, stress response, transcriptional regulation and modulation of apoptosis in autoimmune diseases. Uncovered novel properties of the SRP components present a new perspective for the mammalian SRP as a biological modulator of multiple cellular processes. As a consequence of these findings, SRP components have been correlated with a growing list of diseases, such as cancer progression, myopathies and bone marrow genetic diseases, suggesting a potential for development of SRP-target therapies of each individual component. For the first time, here we present the current knowledge on the SRP noncanonical functions and raise the need of a deeper understanding of the molecular interactions between SRP and accessory cellular components. We examine diseases associated with SRP components and discuss the development and feasibility of therapeutics targeting individual SRP noncanonical functions.
Collapse
Affiliation(s)
- Camilla Faoro
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Sandro F Ataide
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
6
|
Koczkodaj D, Muzyka-Kasietczuk J, Chocholska S, Podhorecka M. Prognostic significance of isochromosome 17q in hematologic malignancies. Oncotarget 2021; 12:708-718. [PMID: 33868591 PMCID: PMC8021031 DOI: 10.18632/oncotarget.27914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/19/2021] [Indexed: 11/29/2022] Open
Abstract
Isochromosome 17q [i(17q)] with its two identical long arms is formed by duplication of the q arm and loss of the short p arm. The breakpoint in chromosome 17 that allows the formation of this isochromosome is located at 17p11.2, and the ~240 kb region with its large, palindromic, low-copy repeat sequences are present here. The region is highly unstable and susceptible to a variety of genomic alterations which may be induced by or without toxic agents. One molecular consequence of i(17q) development is the obligatory loss of a single TP53 allele of the tumor suppressor P53 protein located at 17p13.1. Isochromosome 17q is involved in cancer development and progression. It occurs in combination with other chromosomal defects (complex cytogenetics), and rarely as a single mutation. The i(17q) rearrangement has been described as the most common chromosomal aberration in primitive neuroectodermal tumors and medulloblastomas. This isochromosome is also detected in different hematological disorders. In this article, we analyze literature data on the presence of i(17q) in proliferative disorders of the hematopoietic system in the context of its role as a prognostic factor of disease progression. The case reports are added to support the presented data. Currently, there are no indications for the use of specific treatment regimens in the subjects with a presence of the isochromosome 17q. Thus, it is of importance to continue studies on the prognostic role of this abnormality and even single cases should be reported as they may be used for further statistical analyses or meta-analyses.
Collapse
Affiliation(s)
- Dorota Koczkodaj
- Department of Cancer Genetics with the Cytogenetic Laboratory, Medical University of Lublin, Lublin, Poland
| | - Justyna Muzyka-Kasietczuk
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Sylwia Chocholska
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Monika Podhorecka
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| |
Collapse
|
7
|
Peter B, Scherer N, Liang WS, Pophal S, Nielsen C, Grebe TA. A phenotypically diverse family with an atypical 22q11.2 deletion due to an unbalanced 18q23;22q11.2 translocation. Am J Med Genet A 2021; 185:1532-1537. [PMID: 33569883 DOI: 10.1002/ajmg.a.62121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/03/2021] [Accepted: 01/24/2021] [Indexed: 11/08/2022]
Abstract
The 22q11.2 deletion syndrome (22q11.2 DS) is the most common deletion syndrome in humans. In most cases, it occurs de novo. A rare family of three with 22q11.2 deletion syndrome (22q11.2 DS) resulting from an unbalanced 18q;22q translocation is reported here. Their deletion region is atypical in that it includes only 26 of the 36 genes in the minimal critical 22q11.2 DS region but it involves the loss of the centromeric 22q region and the entire p arm. The deletion region overlaps with seven other rare atypical cases; common to all cases was the loss of a region including SEPT5-GP1BB proximally and most of ARVCF distally. Interrogation of the deleted 22q region proximal to the canonical 22q11.2 deletion region in the DECIPHER database showed seven cases with isolated or combined traits of 22q11.2 DS, including three with clefts. The phenotypes in the present family thus may result from the loss of a subset of genes in the critical region, or alternatively the loss of other genes or sequences in the proximal 22q deletion region, or interactive effects among these. Despite the identical deletion locus in the three affected family members, expression of the 22q11.2 DS traits differed substantially among them. These three related cases thus contribute to knowledge of 22q11.2 DS in that their unusual deletion locus co-occurred with the cardinal features of the syndrome while their identical deletions are associated with variable phenotypic expression.
Collapse
Affiliation(s)
- Beate Peter
- Speech and Hearing Science, College of Health Solutions, Arizona State University, Tempe, Arizona, USA.,Department of Communication Sciences and Disorders, Saint Louis University, Saint Louis, Missouri, USA
| | - Nancy Scherer
- Speech and Hearing Science, College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Stephen Pophal
- Phoenix Children's Hospital, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Colby Nielsen
- College of Medicine, University of Arizona, Phoenix, Arizona, USA
| | - Theresa A Grebe
- Phoenix Children's Hospital, University of Arizona College of Medicine, Phoenix, Arizona, USA
| |
Collapse
|
8
|
Javed S, Selliah T, Lee YJ, Huang WH. Dosage-sensitive genes in autism spectrum disorders: From neurobiology to therapy. Neurosci Biobehav Rev 2020; 118:538-567. [PMID: 32858083 DOI: 10.1016/j.neubiorev.2020.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/26/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of heterogenous neurodevelopmental disorders affecting 1 in 59 children. Syndromic ASDs are commonly associated with chromosomal rearrangements or dosage imbalance involving a single gene. Many of these genes are dosage-sensitive and regulate transcription, protein homeostasis, and synaptic function in the brain. Despite vastly different molecular perturbations, syndromic ASDs share core symptoms including social dysfunction and repetitive behavior. However, each ASD subtype has a unique pathogenic mechanism and combination of comorbidities that require individual attention. We have learned a great deal about how these dosage-sensitive genes control brain development and behaviors from genetically-engineered mice. Here we describe the clinical features of eight monogenic neurodevelopmental disorders caused by dosage imbalance of four genes, as well as recent advances in using genetic mouse models to understand their pathogenic mechanisms and develop intervention strategies. We propose that applying newly developed quantitative molecular and neuroscience technologies will advance our understanding of the unique neurobiology of each disorder and enable the development of personalized therapy.
Collapse
Affiliation(s)
- Sehrish Javed
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Tharushan Selliah
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu-Ju Lee
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Wei-Hsiang Huang
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada.
| |
Collapse
|
9
|
Scott J, Thakar S, Mao Y, Qin H, Hejran H, Lee SY, Yu T, Klezovitch O, Cheng H, Mu Y, Ghosh S, Vasioukhin V, Zou Y. Apical-Basal Polarity Signaling Components, Lgl1 and aPKCs, Control Glutamatergic Synapse Number and Function. iScience 2019; 20:25-41. [PMID: 31546104 PMCID: PMC6817635 DOI: 10.1016/j.isci.2019.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/25/2019] [Accepted: 09/04/2019] [Indexed: 12/17/2022] Open
Abstract
Normal synapse formation is fundamental to brain function. We show here that an apical-basal polarity (A-BP) protein, Lgl1, is present in the postsynaptic density and negatively regulates glutamatergic synapse numbers by antagonizing the atypical protein kinase Cs (aPKCs). A planar cell polarity protein, Vangl2, which inhibits synapse formation, was decreased in synaptosome fractions of cultured cortical neurons from Lgl1 knockout embryos. Conditional knockout of Lgl1 in pyramidal neurons led to reduction of AMPA/NMDA ratio and impaired plasticity. Lgl1 is frequently deleted in Smith-Magenis syndrome (SMS). Lgl1 conditional knockout led to increased locomotion, impaired novel object recognition and social interaction. Lgl1+/- animals also showed increased synapse numbers, defects in open field and social interaction, as well as stereotyped repetitive behavior. Social interaction in Lgl1+/- could be rescued by NMDA antagonists. Our findings reveal a role of apical-basal polarity proteins in glutamatergic synapse development and function and also suggest a potential treatment for SMS patients with Lgl1 deletion.
Collapse
Affiliation(s)
- John Scott
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sonal Thakar
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ye Mao
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Huaping Qin
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - Helen Hejran
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - Su-Yee Lee
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ting Yu
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olga Klezovitch
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Hongqiang Cheng
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yongxin Mu
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sourav Ghosh
- Department of Neurology, Yale University, New Haven, CT 06511, USA
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yimin Zou
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
10
|
Kaplan K, McCool C, Lupski JR, Glaze D, Potocki L. Objective measures of sleep disturbances in children with Potocki-Lupski syndrome. Am J Med Genet A 2019; 179:1982-1986. [PMID: 31342617 DOI: 10.1002/ajmg.a.61307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 11/06/2022]
Abstract
Potocki-Lupski syndrome (PTLS; MIM 610883) is a neurodevelopmental disorder caused by a microduplication, a 3.7 Mb copy number variant, mapping within chromosome 17p11.2, encompassing the dosage-sensitive RAI1 gene. Whereas RAI1 triplosensitivity causes PTLS, haploinsufficiency of RAI1 due to 17p11.2 microdeletion causes the clinically distinct Smith-Magenis syndrome (SMS; MIM 182290). Most individuals with SMS have an inversion of the melatonin cycle. Subjects with PTLS have mild sleep disturbances such as sleep apnea with no melatonin abnormalities described. Sleep patterns and potential disturbances in subjects with PTLS have not been objectively characterized. We delineated sleep characteristics in 23 subjects with PTLS who underwent a polysomnogram at Texas Children's Hospital. Eleven of these subjects (58%) completed the Child's Sleep Habits Questionnaire (CSHQ). Urinary melatonin was measured in one patient and published previously. While the circadian rhythm of melatonin in PTLS appears not to be disrupted, we identified significant differences in sleep efficiency, percentage of rapid eye movement sleep, oxygen nadir, obstructive apnea hypopnea index, and periodic limb movements between prepubertal subjects with PTLS and previously published normative data. Data from the CSHQ indicate that 64% (7/11) of parents do not identify a sleep disturbance in their children. Our data indicate that younger individuals, <10 years, with PTLS have statistically significant abnormalities in five components of sleep despite lack of recognition of substantial sleep disturbances by parents. Our data support the contention that patients with PTLS should undergo clinical evaluations for sleep disordered breathing and periodic limb movement disorder, both of which are treatable conditions.
Collapse
Affiliation(s)
- Kevin Kaplan
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Children's Sleep Center, Baylor College of Medicine, Houston, Texas.,Department of Pulmonary, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Caroline McCool
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Daniel Glaze
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Children's Sleep Center, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Neurology, Baylor College of Medicine, Houston, Texas
| | - Lorraine Potocki
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
11
|
Lupski JR. 2018 Victor A. McKusick Leadership Award: Molecular Mechanisms for Genomic and Chromosomal Rearrangements. Am J Hum Genet 2019; 104:391-406. [PMID: 30849326 PMCID: PMC6407437 DOI: 10.1016/j.ajhg.2018.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA.
| |
Collapse
|
12
|
|
13
|
Rajeh A, Lv J, Lin Z. Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota. BMC Genomics 2018; 19:282. [PMID: 29690866 PMCID: PMC5937819 DOI: 10.1186/s12864-018-4683-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 01/06/2023] Open
Abstract
Background Chromosomal rearrangements have been shown to facilitate speciation through creating a barrier of gene flow. However, it is not known whether heterogeneous rates of chromosomal rearrangement at the genome scale contributed to the huge disparity of species richness among different groups of organisms, which is one of the most remarkable and pervasive patterns on Earth. The largest fungal phylum Ascomycota is an ideal study system to address this question because it comprises three subphyla (Saccharomycotina, Taphrinomycotina, and Pezizomycotina) whose species numbers differ by two orders of magnitude (59,000, 1000, and 150 respectively). Results We quantified rates of genome rearrangement for 71 Ascomycota species that have well-assembled genomes. The rates of inter-species genome rearrangement, which were inferred based on the divergence rates of gene order, are positively correlated with species richness at both ranks of subphylum and class in Ascomycota. This finding is further supported by our quantification of intra-species rearrangement rates based on paired-end genome sequencing data of 216 strains from three representative species, suggesting a difference of intrinsic genome instability among Ascomycota lineages. Our data also show that different rates of imbalanced rearrangements, such as deletions, are a major contributor to the heterogenous rearrangement rates. Conclusions Various lines of evidence in this study support that a higher rate of rearrangement at the genome scale might have accelerated the speciation process and increased species richness during the evolution of Ascomycota species. Our findings provide a plausible explanation for the species disparity among Ascomycota lineages, which will be valuable to unravel the underlying causes for the huge disparity of species richness in various taxonomic groups. Electronic supplementary material The online version of this article (10.1186/s12864-018-4683-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ahmad Rajeh
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.,Department of Computer Science, Saint Louis University, St. Louis, MO, 63103, USA
| | - Jie Lv
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.
| |
Collapse
|
14
|
Bissell S, Wilde L, Richards C, Moss J, Oliver C. The behavioural phenotype of Potocki-Lupski syndrome: a cross-syndrome comparison. J Neurodev Disord 2018; 10:2. [PMID: 29329513 PMCID: PMC5795277 DOI: 10.1186/s11689-017-9221-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 12/19/2017] [Indexed: 01/06/2023] Open
Abstract
Background Potocki-Lupski syndrome (PTLS) and Smith-Magenis syndrome (SMS) are related genomic disorders, as duplication 17p11.2 (associated with PTLS) is the reciprocal recombination product of the SMS microdeletion. While SMS has a relatively well-delineated behavioural phenotype, the behavioural profile in PTLS is less well defined, despite purported associations with autism spectrum disorder (ASD) and the suggestion that some behaviours may be diametric to those seen in SMS. Methods Caregivers of individuals with PTLS (N = 34; M age = 12.43, SD = 6.78) completed online behavioural questionnaires, including the Challenging Behaviour Questionnaire (CBQ), the Activity Questionnaire (TAQ), the Repetitive Behaviour Questionnaire (RBQ), the Mood, Interest and Pleasure Questionnaire-Short Form (MIPQ-S) and the Social Communication Questionnaire (SCQ), which assesses behaviours associated with ASD. Individuals with PTLS were matched on age and adaptive functioning to individuals with SMS (N = 31; M age = 13.61, SD = 6.85) and individuals with idiopathic ASD (N = 33; M age = 12.04, SD = 5.85) from an existing dataset. Results Individuals with PTLS and SMS were less impaired than those with idiopathic ASD on the communication and reciprocal social interaction subscales of the SCQ, but neither syndrome group differed from idiopathic ASD on the restricted, repetitive and stereotyped behaviours subscale. On the repetitive behaviour measure, individuals with PTLS and idiopathic ASD scored higher than individuals with SMS on the compulsive behaviour subscale. Rates of self-injury and property destruction were significantly lower in PTLS and idiopathic ASD than in SMS. No between-syndrome differences were found in relation to overactivity or mood; however, impulsivity was greater in SMS than in PTLS. Conclusions Findings suggest some overlap in the behavioural phenotype of PTLS and features of ASD symptomatology; however, the overall profile of behaviours in PTLS appears to be divergent from both idiopathic ASD and SMS. Relative to idiopathic ASD, PTLS is not characterised by communication or social interaction deficits. However, restricted and repetitive behaviours were evident in PTLS, and these may be characterised specifically by compulsive behaviours. While several behavioural differences were identified between PTLS and SMS, there was little evidence of diametric behavioural phenotypes, particularly in relation to social behaviour.
Collapse
Affiliation(s)
- Stacey Bissell
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Lucy Wilde
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, B15 2TT, UK
| | - Caroline Richards
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jo Moss
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Cognitive Neuroscience, University College London, Alexandra House, 17-19 Queen Square, London, WC1N 3AR, UK
| | - Chris Oliver
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, B15 2TT, UK
| |
Collapse
|
15
|
Abstract
Smith-Magenis syndrome (SMS; OMIM #182290) is a complex genetic disorder characterized by distinctive physical features, developmental delay, cognitive impairment, and a typical behavioral phenotype. SMS is caused by interstitial 17p11.2 deletions, encompassing multiple genes and including the retinoic acid-induced 1 gene (RAI1), or by mutations in RAI1 itself. About 10% of all the SMS patients, in fact, carry an RAI1 mutation responsible for the phenotype. RAI1 (OMIM *607642) is a dosage-sensitive gene expressed in many tissues and highly conserved among species. Over the years, several studies have demonstrated that RAI1 (or its homologs in animal models) acts as a transcriptional factor implicated in embryonic neurodevelopment, neuronal differentiation, cell growth and cell cycle regulation, bone and skeletal development, lipid and glucose metabolisms, behavioral functions, and circadian activity. Patients with RAI1 pathogenic variants show some phenotypic differences when compared to those carrying the typical deletion. They usually have lower incidence of hypotonia and less cognitive impairment than those with 17p11.2 deletions but more frequently show the behavioral characteristics of the syndrome and overeating issues. These differences reflect the primary pathogenetic role of RAI1 without the pathogenetic contribution of the other genes included in the typical 17p11.2 deletion. The better comprehension of physiological roles of RAI1, its molecular co-workers and interactors, and its contribution in determining the typical SMS phenotype will certainly open a new path for therapeutic interventions.
Collapse
Affiliation(s)
- Mariateresa Falco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Sonia Amabile
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Naples, Italy
| | - Fabio Acquaviva
- Department of Translational Medical Sciences (DISMET), Section of Pediatric Clinical Genetics, University of Naples “Federico II”, Naples, Italy
| |
Collapse
|
16
|
Mendez-Rosado LA, Lantigua A, Galarza J, Hamid Al-Rikabi AB, Ziegler M, Liehr T. Unusual de novo Partial Trisomy 17p12p11.2 due to Unbalanced Insertion into 5p13.1 in a Severely Affected Boy. J Pediatr Genet 2017; 6:165-168. [PMID: 28794908 DOI: 10.1055/s-0037-1599195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Gain of copy numbers can be due to different chromosomal rearrangements such as direct or indirect duplications, translocations, small supernumerary marker chromosomes, or insertions. In a 3-year-old boy with dysmorphic features and developmental delay, chromosome analyses revealed a derivative chromosome 5. Microdissection and reverse fluorescence in situ hybridization identified the in 5p13.1 inserted part as 17p12-p11.2 material. Thus the patient suffered from a rare combination of genomic disorder, that is, Charcot-Marie-Tooth disease type 1A and Potocki-Lupski syndrome. Parental studies indicated that the abnormality was de novo in origin. As the question how this rearrangement arose cannot be answered conclusively, formal genetic counseling is warranted, which includes a discussion regarding the possibility of gonadal mosaicism. In conclusion, this case highlights that chromosome 17p is genetically relatively instable, and thus it can lead to rare chromosomal conditions.
Collapse
Affiliation(s)
| | | | | | - Ahmed B Hamid Al-Rikabi
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Monika Ziegler
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| |
Collapse
|
17
|
Mullegama SV, Alaimo JT, Fountain MD, Burns B, Balog AH, Chen L, Elsea SH. RAI1 Overexpression Promotes Altered Circadian Gene Expression and Dyssomnia in Potocki-Lupski Syndrome. J Pediatr Genet 2017; 6:155-164. [PMID: 28794907 DOI: 10.1055/s-0037-1599147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Retinoic acid induced 1 ( RAI1 ) encodes a dosage-sensitive gene that when haploinsufficient results in Smith-Magenis syndrome (SMS) and when overexpressed results in Potocki-Lupski syndrome (PTLS). Phenotypic and molecular evidence illustrates that haploinsufficiency of RAI1 disrupts circadian rhythm through the dysregulation of the master circadian regulator, circadian locomotor output cycles kaput ( CLOCK) , and other core circadian components, contributing to prominent sleep disturbances in SMS. However, the phenotypic and molecular characterization of sleep features in PTLS has not been elucidated. Using the Pittsburgh Sleep Quality Index (PSQI), caregivers of 15 school-aged children with PTLS reported difficulties in initiating sleep. Indeed, more than 70% of individuals manifested moderate to severe sleep latency, as defined by the PSQI. Moreover, these individuals manifested difficulties in sleep maintenance, with middle of the night and early morning awakenings. When assessing daytime sleepiness through the Epworth Sleepiness Scale, approximately 21% of the individuals manifested excessive daytime somnolence. This indicates that mild dyssomnia characterizes the majority of the sleep phenotype, with occasionally problematic daytime somnolence, a phenotype different than that expressed by individuals with SMS, where daytime sleepiness is a chronic problem. Gene expression analysis of the core circadian machinery in the hypothalamus of the PTLS mouse model ( Rai1 -Tg) found significant dysregulation of the transcriptional activators, Clock and Arntl , and the transcriptional repressors, Per1-3 and Cry1/2 , during both light and dark phases. These findings suggest a partial loss of circadian entrainment typically evoked by environmental photic cues. Examination of circadian clock gene expression in the Rai1- Tg mouse heart, liver, and kidney found unchanged expression of Clock and most of its downstream targets during both light and dark phases, suggesting an asynchronized circadian rhythm. Furthermore, examination of circadian gene expression in synchronized PTLS lymphoblasts revealed reduced transcripts of the Period ( PER1-3 ) family and normal expression of CRY1/2 . The finding that central circadian gene expression was altered while many peripheral circadian components were intact suggests a tissue-specific circadian uncoupling of the circadian machinery due to Rai1 overexpression. Overall, our results demonstrate that overexpression of RAI1 results in sleep deficiencies in individuals with PTLS due to a lack of properly regulated circadian machinery gene expression and highlight the importance of evaluating sleep concerns in individuals with PTLS.
Collapse
Affiliation(s)
- Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, United States
| | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Michael D Fountain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Brooke Burns
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States
| | - Amanda Hebert Balog
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States
| | - Li Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, United States.,Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States
| |
Collapse
|
18
|
Loviglio MN, Beck CR, White JJ, Leleu M, Harel T, Guex N, Niknejad A, Bi W, Chen ES, Crespo I, Yan J, Charng WL, Gu S, Fang P, Coban-Akdemir Z, Shaw CA, Jhangiani SN, Muzny DM, Gibbs RA, Rougemont J, Xenarios I, Lupski JR, Reymond A. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. Genome Med 2016; 8:105. [PMID: 27799067 PMCID: PMC5088687 DOI: 10.1186/s13073-016-0359-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/16/2016] [Indexed: 02/13/2023] Open
Abstract
Background Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. Methods We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes. Results Potentially deleterious variants were identified in nine of these individuals using whole-exome sequencing. Eight of these changes affect KMT2D, ZEB2, MAP2K2, GLDC, CASK, MECP2, KDM5C, and POGZ, known to be associated with Kabuki syndrome 1, Mowat-Wilson syndrome, cardiofaciocutaneous syndrome, glycine encephalopathy, mental retardation and microcephaly with pontine and cerebellar hypoplasia, X-linked mental retardation 13, X-linked mental retardation Claes-Jensen type, and White-Sutton syndrome, respectively. The ninth individual carries a de novo variant in JAKMIP1, a regulator of neuronal translation that was recently found deleted in a patient with autism spectrum disorder. Analyses of co-expression and biomedical text mining suggest that these pathologies and SMS are part of the same disease network. Further support for this hypothesis was obtained from transcriptome profiling that showed that the expression levels of both Zeb2 and Map2k2 are perturbed in Rai1–/– mice. As an orthogonal approach to potentially contributory disease gene variants, we used chromatin conformation capture to reveal chromatin contacts between RAI1 and the loci flanking ZEB2 and GLDC, as well as between RAI1 and human orthologs of the genes that show perturbed expression in our Rai1–/– mouse model. Conclusions These holistic studies of RAI1 and its interactions allow insights into SMS and other disorders associated with intellectual disability and behavioral abnormalities. Our findings support a pan-genomic approach to the molecular diagnosis of a distinctive disorder. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0359-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Maria Nicla Loviglio
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marion Leleu
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicolas Guex
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Anne Niknejad
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Crespo
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Jiong Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Laboratory Medicine Program, UHN, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5G 2C4, Canada
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Fang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: WuXiNextCODE, 101Main Street, Cambridge, MA, 02142, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacques Rougemont
- School of Life Sciences, EPFL (Ecole Polytechnique Fédérale de Lausanne), 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
| |
Collapse
|
19
|
Acquaviva F, Sana ME, Della Monica M, Pinelli M, Postorivo D, Fontana P, Falco MT, Nardone AM, Lonardo F, Iascone M, Scarano G. First evidence of Smith-Magenis syndrome in mother and daughter due to a novel RAI mutation. Am J Med Genet A 2016; 173:231-238. [PMID: 27683195 DOI: 10.1002/ajmg.a.37989] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022]
Abstract
Smith-Magenis syndrome (SMS) is a complex genetic disorder caused by interstitial 17p11.2 deletions encompassing multiple genes, including the retinoic acid induced 1 gene-RAI1-or mutations in RAI1 itself. The clinical spectrum includes developmental delay, cognitive impairment, and behavioral abnormalities, with distinctive physical features that become more evident with age. No patients have been reported to have had offspring. We here describe a girl with developmental delay, mainly compromising the speech area, and her mother with mild intellectual disabilities and minor dysmorphic features. Both had sleep disturbance and attention deficit disorder, but no other atypical behaviors have been reported. In both, CGH-array analysis detected a 15q13.3 interstitial duplication, encompassing CHRNA7. However, the same duplication has been observed in several, apparently healthy, maternal relatives. We, thus, performed a whole exome sequencing analysis, which detected a frameshift mutation in RAI1, de novo in the mother, and transmitted to her daughter. No other family members carried this mutation. This is the first report of an SMS patient having offspring. Our experience confirms the importance of searching for alternative causative genetic mechanisms in case of confounding/inconclusive findings such as a CGH-array result of uncertain significance. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Fabio Acquaviva
- U.O. di Genetica Medica, A.O.R.N. "G. Rummo", Benevento, Italy
| | - Maria Elena Sana
- U.S.S.D. Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Michele Pinelli
- Telethon Institute of Genetic Medicine (TIGEM), Pozzuoli, Napoli, Italy
| | - Diana Postorivo
- U.O.C. Laboratorio di Genetica Medica, Policlinico Tor Vergata, Roma, Italy
| | - Paolo Fontana
- Dipartimento di Medicine Molecolare e Biotecnologie Mediche, Università "Federico II", Napoli, Italy
| | - Maria Teresa Falco
- Dipartimento di Medicine Molecolare e Biotecnologie Mediche, Università "Federico II", Napoli, Italy
| | - Anna Maria Nardone
- U.O.C. Laboratorio di Genetica Medica, Policlinico Tor Vergata, Roma, Italy
| | | | - Maria Iascone
- U.S.S.D. Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | |
Collapse
|
20
|
Yuan B, Neira J, Gu S, Harel T, Liu P, Briceño I, Elsea SH, Gómez A, Potocki L, Lupski JR. Nonrecurrent PMP22-RAI1 contiguous gene deletions arise from replication-based mechanisms and result in Smith-Magenis syndrome with evident peripheral neuropathy. Hum Genet 2016; 135:1161-74. [PMID: 27386852 DOI: 10.1007/s00439-016-1703-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/21/2016] [Indexed: 11/29/2022]
Abstract
Hereditary neuropathy with liability to pressure palsies (HNPP) and Smith-Magenis syndrome (SMS) are genomic disorders associated with deletion copy number variants involving chromosome 17p12 and 17p11.2, respectively. Nonallelic homologous recombination (NAHR)-mediated recurrent deletions are responsible for the majority of HNPP and SMS cases; the rearrangement products encompass the key dosage-sensitive genes PMP22 and RAI1, respectively, and result in haploinsufficiency for these genes. Less frequently, nonrecurrent genomic rearrangements occur at this locus. Contiguous gene duplications encompassing both PMP22 and RAI1, i.e., PMP22-RAI1 duplications, have been investigated, and replication-based mechanisms rather than NAHR have been proposed for these rearrangements. In the current study, we report molecular and clinical characterizations of six subjects with the reciprocal phenomenon of deletions spanning both genes, i.e., PMP22-RAI1 deletions. Molecular studies utilizing high-resolution array comparative genomic hybridization and breakpoint junction sequencing identified mutational signatures that were suggestive of replication-based mechanisms. Systematic clinical studies revealed features consistent with SMS, including features of intellectual disability, speech and gross motor delays, behavioral problems and ocular abnormalities. Five out of six subjects presented clinical signs and/or objective electrophysiologic studies of peripheral neuropathy. Clinical profiling may improve the clinical management of this unique group of subjects, as the peripheral neuropathy can be more severe or of earlier onset as compared to SMS patients having the common recurrent deletion. Moreover, the current study, in combination with the previous report of PMP22-RAI1 duplications, contributes to the understanding of rare complex phenotypes involving multiple dosage-sensitive genes from a genetic mechanistic standpoint.
Collapse
Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juanita Neira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ignacio Briceño
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
- Instituto de Referencia Andino, Bogotá, Colombia
- Facultad de Medicina, Universidad de La Sabana, Chía, Colombia
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alberto Gómez
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
- Instituto de Referencia Andino, Bogotá, Colombia
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Texas Children's Hospital, Houston, TX, 77030, USA.
| |
Collapse
|
21
|
Gupta R, Gupta N, Nampoothiri S, Mandal K, Kishore Y, Sharma P, Kabra M, Phadke SR. Smith-Magenis Syndrome: Face Speaks. Indian J Pediatr 2016; 83:589-93. [PMID: 26676648 DOI: 10.1007/s12098-015-1940-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/26/2015] [Indexed: 11/26/2022]
Abstract
Smith-Magenis syndrome is a well delineated microdeletion syndrome with characteristic facial and behavioral phenotype. With the availability of the multi-targeted molecular cytogenetic techniques like Multiplex Ligation Probe Amplification and cytogenetic microarray, the cases are diagnosed even without clinical suspicion. Here, the authors present clinical features of nine Indian cases of Smith-Magenis syndrome. Characteristic facial phenotype including tented upper lip, broad forehead, midface hypoplasia, short philtrum and upslant of palpebral fissure is obvious in the photographs. The behavioral variations were seen in some of the cases but were not the presenting features. The characteristic facial phenotype can be an important clinical guide to the diagnosis.
Collapse
Affiliation(s)
- Rekha Gupta
- Department of Medical Genetics, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, AIMS Ponekkara, Cochin, Kerala, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Raibereli Road, Lucknow, Uttar Pradesh, 226014, India
| | - Yougal Kishore
- Department of Medical Genetics, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Raibereli Road, Lucknow, Uttar Pradesh, 226014, India
| | - Pankaj Sharma
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Raibereli Road, Lucknow, Uttar Pradesh, 226014, India.
| |
Collapse
|
22
|
Tsou JH, Yang YC, Pao PC, Lin HC, Huang NK, Lin ST, Hsu KS, Yeh CM, Lee KH, Kuo CJ, Yang DM, Lin JH, Chang WC, Lee YC. Important Roles of Ring Finger Protein 112 in Embryonic Vascular Development and Brain Functions. Mol Neurobiol 2016; 54:2286-2300. [PMID: 26951452 DOI: 10.1007/s12035-016-9812-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 11/28/2022]
Abstract
Rnf112 is a member of the RING finger protein family. The expression of Rnf112 is abundant in the brain and is regulated during brain development. Our previous study has revealed that Rnf112 can promote neuronal differentiation by inhibiting the progression of the cell cycle in cell models. In this study, we further revealed the important functions of Rnf112 in embryo development and in adult brain. Our data showed that most of the Rnf112 -/- embryos exhibited blood vascular defects and died in utero. Upon further investigation, we found that the survival rate of homozygous Rnf112 knockout mice in 129/sv and C57BL/6 mixed genetic background was increased. The survived newborns of Rnf112 -/- mice manifested growth retardation as indicated by smaller size and a reduced weight. Although the overall organization of the brain did not appear to be severely affected in Rnf112 -/- mice, using in vivo 3D MRI imaging, we found that when compared to wild-type littermates, brains of Rnf112 -/- mice were smaller. In addition, Rnf112 -/- mice displayed impairment of brain functions including motor balance, and spatial learning and memory. Our results provide important aspects for the study of Rnf112 gene functions.
Collapse
Affiliation(s)
- Jen-Hui Tsou
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ying-Chen Yang
- Department of Biotechnology and Animal Science, College of Bioresources, National Ilan University, Ilan, Taiwan
| | - Ping-Chieh Pao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hui-Ching Lin
- Department and Institute of Physiology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Nai-Kuei Huang
- National Research Institute of Chinese Medicine, Taipei, Taiwan.,Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Shih-Ting Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuei-Sen Hsu
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Che-Ming Yeh
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chu-Jen Kuo
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan.,Department of Radiology, Shin Kong Wu Ho-Su Memorial Hospital, School of Medicine, Fu Jen Catholic University, Taipei, Taiwan
| | - De-Ming Yang
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Biophotonics, School of Medical Technology and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Jiann-Her Lin
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Wen-Chang Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Chao Lee
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan. .,Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, Taiwan.
| |
Collapse
|
23
|
Kurtovic-Kozaric A, Mehinovic L, Stomornjak-Vukadin M, Kurtovic-Basic I, Catibusic F, Kozaric M, Mesihovic-Dinarevic S, Hasanhodzic M, Glamuzina D. Diagnostics of common microdeletion syndromes using fluorescence in situ hybridization: single center experience in a developing country. Bosn J Basic Med Sci 2016; 16:121-5. [PMID: 26937776 PMCID: PMC4852993 DOI: 10.17305/bjbms.2016.994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 12/14/2022] Open
Abstract
Microdeletion syndromes are caused by chromosomal deletions of less than 5 megabases which can be detected by fluorescence in situ hybridization (FISH). We evaluated the most commonly detected microdeletions for the period from June 01, 2008 to June 01, 2015 in the Federation of Bosnia and Herzegovina, including DiGeorge, Prader-Willi/Angelman, Wolf-Hirschhorn, and Williams syndromes. We report 4 patients with DiGeorge syndromes, 4 patients with Prader-Willi/Angelman, 4 patients with Wolf-Hirschhorn syndrome, and 3 patients with Williams syndrome in the analyzed 7 year period. Based on the positive FISH results for each syndrome, the incidence was calculated for the Federation of Bosnia and Herzegovina. These are the first reported frequencies of the microdeletion syndromes in the Federation of Bosnia and Herzegovina.
Collapse
|
24
|
Yuan B, Liu P, Gupta A, Beck CR, Tejomurtula A, Campbell IM, Gambin T, Simmons AD, Withers MA, Harris RA, Rogers J, Schwartz DC, Lupski JR. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. PLoS Genet 2015; 11:e1005686. [PMID: 26641089 PMCID: PMC4671654 DOI: 10.1371/journal.pgen.1005686] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 10/29/2015] [Indexed: 11/30/2022] Open
Abstract
Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. Genomic instability due to the intrinsic sequence architecture of the genome, such as low copy repeats (LCRs), is a major contributor to de novo mutations that can occur in the process of human genome evolution. LCRs can mediate genomic rearrangements associated with genomic disorders by acting as substrates for nonallelic homologous recombination. Juvenile-onset nephronophthisis 1 is the most frequent genetic cause of renal failure in children. An LCR-mediated, homozygous common recurrent deletion encompassing NPHP1 is found in the majority of affected subjects, while heterozygous deletion representing the nephronophthisis 1 recessive carrier state is frequently observed amongst world populations. Interestingly, the human NPHP1 locus is located proximal to the head-to-head fusion site of two ancestral chromosomes that occurred in the great apes, which resulted in a reduction of chromosome number from 48 in nonhuman primates to the current 46 in humans. In this study, we characterized and provided evidence for the diverse genomic architecture at the NPHP1 locus and potential structural variant haplotypes in the human population. Furthermore, our analyses of primate genomes shed light on the massive changes of genomic architecture at the human NPHP1 locus and delineated a model for the emergence of the LCRs during primate evolution.
Collapse
Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Aditya Gupta
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christine R. Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anusha Tejomurtula
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ian M. Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alexandra D. Simmons
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marjorie A. Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jeffrey Rogers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
25
|
Sekan AS, Isayenkov SV, Blume YB. Development of marker-free transformants by site-specific recombinases. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715060080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
26
|
Yuan B, Harel T, Gu S, Liu P, Burglen L, Chantot-Bastaraud S, Gelowani V, Beck C, Carvalho C, Cheung S, Coe A, Malan V, Munnich A, Magoulas P, Potocki L, Lupski J. Nonrecurrent 17p11.2p12 Rearrangement Events that Result in Two Concomitant Genomic Disorders: The PMP22-RAI1 Contiguous Gene Duplication Syndrome. Am J Hum Genet 2015; 97:691-707. [PMID: 26544804 DOI: 10.1016/j.ajhg.2015.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
Abstract
The genomic duplication associated with Potocki-Lupski syndrome (PTLS) maps in close proximity to the duplication associated with Charcot-Marie-Tooth disease type 1A (CMT1A). PTLS is characterized by hypotonia, failure to thrive, reduced body weight, intellectual disability, and autistic features. CMT1A is a common autosomal dominant distal symmetric peripheral polyneuropathy. The key dosage-sensitive genes RAI1 and PMP22 are respectively associated with PTLS and CMT1A. Recurrent duplications accounting for the majority of subjects with these conditions are mediated by nonallelic homologous recombination between distinct low-copy repeat (LCR) substrates. The LCRs flanking a contiguous genomic interval encompassing both RAI1 and PMP22 do not share extensive homology; thus, duplications encompassing both loci are rare and potentially generated by a different mutational mechanism. We characterized genomic rearrangements that simultaneously duplicate PMP22 and RAI1, including nine potential complex genomic rearrangements, in 23 subjects by high-resolution array comparative genomic hybridization and breakpoint junction sequencing. Insertions and microhomologies were found at the breakpoint junctions, suggesting potential replicative mechanisms for rearrangement formation. At the breakpoint junctions of these nonrecurrent rearrangements, enrichment of repetitive DNA sequences was observed, indicating that they might predispose to genomic instability and rearrangement. Clinical evaluation revealed blended PTLS and CMT1A phenotypes with a potential earlier onset of neuropathy. Moreover, additional clinical findings might be observed due to the extra duplicated material included in the rearrangements. Our genomic analysis suggests replicative mechanisms as a predominant mechanism underlying PMP22-RAI1 contiguous gene duplications and provides further evidence supporting the role of complex genomic architecture in genomic instability.
Collapse
|
27
|
Neira-Fresneda J, Potocki L. Neurodevelopmental Disorders Associated with Abnormal Gene Dosage: Smith-Magenis and Potocki-Lupski Syndromes. J Pediatr Genet 2015; 4:159-67. [PMID: 27617127 DOI: 10.1055/s-0035-1564443] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 12/22/2022]
Abstract
Smith-Magenis syndrome (SMS) and Potocki-Lupski syndrome (PTLS) are reciprocal contiguous gene syndromes within the well-characterized 17p11.2 region. Approximately 3.6 Mb microduplication of 17p11.2, known as PTLS, represents the mechanistically predicted homologous recombination reciprocal of the SMS microdeletion, both resulting in multiple congenital anomalies. Mouse model studies have revealed that the retinoic acid-inducible 1 gene (RAI1) within the SMS and PTLS critical genomic interval is the dosage-sensitive gene responsible for the major phenotypic features in these disorders. Even though PTLS and SMS share the same genomic region, clinical manifestations and behavioral issues are distinct and in fact some mirror traits may be on opposite ends of a given phenotypic spectrum. We describe the neurobehavioral phenotypes of SMS and PTLS patients during different life phases as well as clinical guidelines for diagnosis and a multidisciplinary approach once diagnosis is confirmed by array comparative genomic hybridization or RAI1 gene sequencing. The main goal is to increase awareness of these rare disorders because an earlier diagnosis will lead to more timely developmental intervention and medical management which will improve clinical outcome.
Collapse
Affiliation(s)
- Juanita Neira-Fresneda
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Texas Children's Hospital, Houston, Texas, United States
| |
Collapse
|
28
|
Lupski JR. Structural variation mutagenesis of the human genome: Impact on disease and evolution. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:419-36. [PMID: 25892534 PMCID: PMC4609214 DOI: 10.1002/em.21943] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 05/19/2023]
Abstract
Watson-Crick base-pair changes, or single-nucleotide variants (SNV), have long been known as a source of mutations. However, the extent to which DNA structural variation, including duplication and deletion copy number variants (CNV) and copy number neutral inversions and translocations, contribute to human genome variation and disease has been appreciated only recently. Moreover, the potential complexity of structural variants (SV) was not envisioned; thus, the frequency of complex genomic rearrangements and how such events form remained a mystery. The concept of genomic disorders, diseases due to genomic rearrangements and not sequence-based changes for which genomic architecture incite genomic instability, delineated a new category of conditions distinct from chromosomal syndromes and single-gene Mendelian diseases. Nevertheless, it is the mechanistic understanding of CNV/SV formation that has promoted further understanding of human biology and disease and provided insights into human genome and gene evolution. Environ. Mol. Mutagen. 56:419-436, 2015. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Room 604B, Houston, Texas
| |
Collapse
|
29
|
Iyer J, Girirajan S. Gene discovery and functional assessment of rare copy-number variants in neurodevelopmental disorders. Brief Funct Genomics 2015; 14:315-28. [DOI: 10.1093/bfgp/elv018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
30
|
Thaker VV, Esteves KM, Towne MC, Brownstein CA, James PM, Crowley L, Hirschhorn JN, Elsea SH, Beggs AH, Picker J, Agrawal PB. Whole exome sequencing identifies RAI1 mutation in a morbidly obese child diagnosed with ROHHAD syndrome. J Clin Endocrinol Metab 2015; 100:1723-30. [PMID: 25781356 PMCID: PMC4422892 DOI: 10.1210/jc.2014-4215] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CONTEXT The current obesity epidemic is attributed to complex interactions between genetic and environmental factors. However, a limited number of cases, especially those with early-onset severe obesity, are linked to single gene defects. Rapid-onset obesity with hypothalamic dysfunction, hypoventilation and autonomic dysregulation (ROHHAD) is one of the syndromes that presents with abrupt-onset extreme weight gain with an unknown genetic basis. OBJECTIVE To identify the underlying genetic etiology in a child with morbid early-onset obesity, hypoventilation, and autonomic and behavioral disturbances who was clinically diagnosed with ROHHAD syndrome. Design/Setting/Intervention: The index patient was evaluated at an academic medical center. Whole-exome sequencing was performed on the proband and his parents. Genetic variants were validated by Sanger sequencing. RESULTS We identified a novel de novo nonsense mutation, c.3265 C>T (p.R1089X), in the retinoic acid-induced 1 (RAI1) gene in the proband. Mutations in the RAI1 gene are known to cause Smith-Magenis syndrome (SMS). On further evaluation, his clinical features were not typical of either SMS or ROHHAD syndrome. CONCLUSIONS This study identifies a de novo RAI1 mutation in a child with morbid obesity and a clinical diagnosis of ROHHAD syndrome. Although extreme early-onset obesity, autonomic disturbances, and hypoventilation are present in ROHHAD, several of the clinical findings are consistent with SMS. This case highlights the challenges in the diagnosis of ROHHAD syndrome and its potential overlap with SMS. We also propose RAI1 as a candidate gene for children with morbid obesity.
Collapse
Affiliation(s)
- Vidhu V Thaker
- Division of Endocrinology (V.V.T., J.N.H.), Newborn Medicine (K.M.E., P.B.A.), and Genetics and Genomics (M.C.T., C.A.B., L.C., A.H.B., J.P., P.B.A.), Department of Medicine, and Gene Discovery Core (M.C.T., C.A.B., L.C., A.H.B., J.P., P.B.A.), The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115; Genetics and Metabolism (P.M.J.), Phoenix Children's Hospital, Phoenix, Arizona 85006; and Department of Molecular and Human Genetics (S.H.E.), Baylor College of Medicine, Houston, Texas 77030
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Dosage changes of a segment at 17p13.1 lead to intellectual disability and microcephaly as a result of complex genetic interaction of multiple genes. Am J Hum Genet 2014; 95:565-78. [PMID: 25439725 DOI: 10.1016/j.ajhg.2014.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/03/2014] [Indexed: 11/24/2022] Open
Abstract
The 17p13.1 microdeletion syndrome is a recently described genomic disorder with a core clinical phenotype of intellectual disability, poor to absent speech, dysmorphic features, and a constellation of more variable clinical features, most prominently microcephaly. We identified five subjects with copy-number variants (CNVs) on 17p13.1 for whom we performed detailed clinical and molecular studies. Breakpoint mapping and retrospective analysis of published cases refined the smallest region of overlap (SRO) for microcephaly to a genomic interval containing nine genes. Dissection of this phenotype in zebrafish embryos revealed a complex genetic architecture: dosage perturbation of four genes (ASGR1, ACADVL, DVL2, and GABARAP) impeded neurodevelopment and decreased dosage of the same loci caused a reduced mitotic index in vitro. Moreover, epistatic analyses in vivo showed that dosage perturbations of discrete gene pairings induce microcephaly. Taken together, these studies support a model in which concomitant dosage perturbation of multiple genes within the CNV drive the microcephaly and possibly other neurodevelopmental phenotypes associated with rearrangements in the 17p13.1 SRO.
Collapse
|
32
|
Gómez-Seguí I, Sánchez-Izquierdo D, Barragán E, Such E, Luna I, López-Pavía M, Ibáñez M, Villamón E, Alonso C, Martín I, Llop M, Dolz S, Fuster Ó, Montesinos P, Cañigral C, Boluda B, Salazar C, Cervera J, Sanz MA. Single-nucleotide polymorphism array-based karyotyping of acute promyelocytic leukemia. PLoS One 2014; 9:e100245. [PMID: 24959826 PMCID: PMC4069034 DOI: 10.1371/journal.pone.0100245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/22/2014] [Indexed: 11/29/2022] Open
Abstract
Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), but additional chromosomal abnormalities (ACA) and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A) 6.0 (Affymetrix) in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%): 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH), being a duplication of 8(q24) (23%) and a deletion of 7(q33-qter) (6%) the most frequent copy-number abnormalities (CNA). Four patients (8%) showed CNAs adjacent to the breakpoints of the translocation. We compared our results with other APL series and found that, except for dup(8q24) and del(7q33-qter), ACA were infrequent (≤3%) but most of them recurrent (70%). Interestingly, having CNA or FLT3 mutation were mutually exclusive events. Neither the number of CNA, nor any specific CNA was associated significantly with prognosis. This study has delineated recurrent abnormalities in addition to t(15;17) that may act as secondary events and could explain leukemogenesis in up to 40% of APL cases with no ACA by conventional cytogenetics.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Chromosome Aberrations
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 17
- Female
- Humans
- Karyotyping
- Leukemia, Promyelocytic, Acute/diagnosis
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/mortality
- Loss of Heterozygosity
- Male
- Middle Aged
- Oncogene Proteins, Fusion/genetics
- Polymorphism, Single Nucleotide
- Prognosis
- Translocation, Genetic
- Young Adult
Collapse
Affiliation(s)
- Inés Gómez-Seguí
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | | | - Eva Barragán
- Laboratory of Molecular Biology, Department of Clinical Chemistry, University Hospital La Fe, Valencia, Spain
| | - Esperanza Such
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Irene Luna
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - María López-Pavía
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Mariam Ibáñez
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Eva Villamón
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Carmen Alonso
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Iván Martín
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Marta Llop
- Laboratory of Molecular Biology, Department of Clinical Chemistry, University Hospital La Fe, Valencia, Spain
| | - Sandra Dolz
- Laboratory of Molecular Biology, Department of Clinical Chemistry, University Hospital La Fe, Valencia, Spain
| | - Óscar Fuster
- Laboratory of Molecular Biology, Department of Clinical Chemistry, University Hospital La Fe, Valencia, Spain
| | - Pau Montesinos
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Carolina Cañigral
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Blanca Boluda
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Claudia Salazar
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Jose Cervera
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
- Genetics Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain
- * E-mail: (IGS); (MAS)
| | - Miguel A. Sanz
- Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
- Department of Medicine, University of Valencia, Valencia, Spain
- * E-mail: (IGS); (MAS)
| |
Collapse
|
33
|
Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC. The genetics of microdeletion and microduplication syndromes: an update. Annu Rev Genomics Hum Genet 2014; 15:215-244. [PMID: 24773319 DOI: 10.1146/annurev-genom-091212-153408] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chromosomal abnormalities, including microdeletions and microduplications, have long been associated with abnormal developmental outcomes. Early discoveries relied on a common clinical presentation and the ability to detect chromosomal abnormalities by standard karyotype analysis or specific assays such as fluorescence in situ hybridization. Over the past decade, the development of novel genomic technologies has allowed more comprehensive, unbiased discovery of microdeletions and microduplications throughout the human genome. The ability to quickly interrogate large cohorts using chromosome microarrays and, more recently, next-generation sequencing has led to the rapid discovery of novel microdeletions and microduplications associated with disease, including very rare but clinically significant rearrangements. In addition, the observation that some microdeletions are associated with risk for several neurodevelopmental disorders contributes to our understanding of shared genetic susceptibility for such disorders. Here, we review current knowledge of microdeletion/duplication syndromes, with a particular focus on recurrent rearrangement syndromes.
Collapse
Affiliation(s)
- Corey T Watson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra/CSIC, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.,Centro Nacional de Análisis Genómico, 08023 Barcelona, Spain
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, Washington 98195
| |
Collapse
|
34
|
Dubourg C, Bonnet-Brilhault F, Toutain A, Mignot C, Jacquette A, Dieux A, Gérard M, Beaumont-Epinette MP, Julia S, Isidor B, Rossi M, Odent S, Bendavid C, Barthélémy C, Verloes A, David V. Identification of Nine New RAI1-Truncating Mutations in Smith-Magenis Syndrome Patients without 17p11.2 Deletions. Mol Syndromol 2014; 5:57-64. [PMID: 24715852 DOI: 10.1159/000357359] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
Smith-Magenis syndrome (SMS) is an intellectual disability syndrome with sleep disturbance, self-injurious behaviors and dysmorphic features. It is estimated to occur in 1/25,000 births, and in 90% of cases it is associated with interstitial deletions of chromosome 17p11.2. RAI1 (retinoic acid induced 1; OMIM 607642) mutations are the second most frequent molecular etiology, with this gene being located in the SMS locus at 17p11.2. Here, we report 9 new RAI1-truncating mutations in nonrelated individuals referred for molecular analysis due to a possible SMS diagnosis. None of these patients carried a 17p11.2 deletion. The 9 mutations include 2 nonsense mutations and 7 heterozygous frameshift mutations leading to protein truncation. All mutations map in exon 3 of RAI1 which codes for more than 98% of the protein. RAI1 regulates gene transcription, and its targets are themselves involved in transcriptional regulation, cell growth and cell cycle regulation, bone and skeletal development, lipid and glucide metabolisms, neurological development, behavioral functions, and circadian activity. We report the clinical features of the patients carrying these deleterious mutations in comparison with those of patients carrying 17p11.2 deletions.
Collapse
Affiliation(s)
- C Dubourg
- Laboratoire de Génétique Moléculaire, CHU Pontchaillou, France ; CNRS UMR 6290, IFR140, Université de Rennes 1, France
| | | | - A Toutain
- Génétique, CHRU Bretonneau, Tours, France
| | - C Mignot
- Service de Génétique Clinique, CHU La Pitié Salpêtrière, France ; Service de Neuropédiatrie, APHP, Hôpital Armand Trousseau, France
| | - A Jacquette
- Service de Génétique Clinique, CHU La Pitié Salpêtrière, France
| | - A Dieux
- Service de Génétique Clinique, CHU, Lille, France
| | - M Gérard
- Service de Génétique, CHR Clémenceau, Caen, France
| | | | - S Julia
- Service de Génétique Médicale, CHU Purpan, Toulouse, France
| | - B Isidor
- Service de Génétique Médicale, CHU, Nantes, France
| | - M Rossi
- Service de Génétique Clinique, CHU, Lyon-Bron, France
| | - S Odent
- CNRS UMR 6290, IFR140, Université de Rennes 1, France ; Service de Génétique Médicale, CHU Hôpital Sud, Rennes, Services de, France
| | - C Bendavid
- CNRS UMR 6290, IFR140, Université de Rennes 1, France
| | | | - A Verloes
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - V David
- Laboratoire de Génétique Moléculaire, CHU Pontchaillou, France ; CNRS UMR 6290, IFR140, Université de Rennes 1, France
| |
Collapse
|
35
|
Lin DY, Huang CC, Hsieh YT, Lin HC, Pao PC, Tsou JH, Lai CY, Hung LY, Wang JM, Chang WC, Lee YC. Analysis of the interaction between Zinc finger protein 179 (Znf179) and promyelocytic leukemia zinc finger (Plzf). J Biomed Sci 2013; 20:98. [PMID: 24359566 PMCID: PMC3878200 DOI: 10.1186/1423-0127-20-98] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/17/2013] [Indexed: 01/15/2023] Open
Abstract
Background Zinc finger protein 179 (Znf179), also known as ring finger protein 112 (Rnf112), is a member of the RING finger protein family and plays an important role in neuronal differentiation. To investigate novel mechanisms of Znf179 regulation and function, we performed a yeast two-hybrid screen to identify Znf179-interacting proteins. Results Using a yeast two-hybrid screen, we have identified promyelocytic leukemia zinc finger (Plzf) as a specific interacting protein of Znf179. Further analysis showed that the region containing the first two zinc fingers of Plzf is critical for its interaction with Znf179. Although the transcriptional regulatory activity of Plzf was not affected by Znf179 in the Gal4-dependent transcription assay system, the cellular localization of Znf179 was changed from cytoplasm to nucleus when Plzf was co-expressed. We also found that Znf179 interacted with Plzf and regulated Plzf protein expression. Conclusions Our results showed that Znf179 interacted with Plzf, resulting in its translocation from cytoplasm to the nucleus and increase of Plzf protein abundance. Although the precise nature and role of the Znf179-Plzf interaction remain to be elucidated, both of these two genes are involved in the regulation of neurogenesis. Our finding provides further research direction for studying the molecular functions of Znf179.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yi-Chao Lee
- Ph,D, Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
| |
Collapse
|
36
|
Itsara A, Vissers L, Steinberg K, Meyer K, Zody M, Koolen D, de Ligt J, Cuppen E, Baker C, Lee C, Graves TA, Wilson R, Jenkins R, Veltman J, Eichler E. Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing. Am J Hum Genet 2012; 90:599-613. [PMID: 22482802 DOI: 10.1016/j.ajhg.2012.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/23/2012] [Accepted: 02/16/2012] [Indexed: 01/22/2023] Open
Abstract
Recurrent deletions have been associated with numerous diseases and genomic disorders. Few, however, have been resolved at the molecular level because their breakpoints often occur in highly copy-number-polymorphic duplicated sequences. We present an approach that uses a combination of somatic cell hybrids, array comparative genomic hybridization, and the specificity of next-generation sequencing to determine breakpoints that occur within segmental duplications. Applying our technique to the 17q21.31 microdeletion syndrome, we used genome sequencing to determine copy-number-variant breakpoints in three deletion-bearing individuals with molecular resolution. For two cases, we observed breakpoints consistent with nonallelic homologous recombination involving only H2 chromosomal haplotypes, as expected. Molecular resolution revealed that the breakpoints occurred at different locations within a 145 kbp segment of >99% identity and disrupt KANSL1 (previously known as KANSL1). In the remaining case, we found that unequal crossover occurred interchromosomally between the H1 and H2 haplotypes and that this event was mediated by a homologous sequence that was once again missing from the human reference. Interestingly, the breakpoints mapped preferentially to gaps in the current reference genome assembly, which we resolved in this study. Our method provides a strategy for the identification of breakpoints within complex regions of the genome harboring high-identity and copy-number-polymorphic segmental duplication. The approach should become particularly useful as high-quality alternate reference sequences become available and genome sequencing of individuals' DNA becomes more routine.
Collapse
|
37
|
Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 2012; 22:211-20. [PMID: 22440479 DOI: 10.1016/j.gde.2012.02.012] [Citation(s) in RCA: 245] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 01/07/2023]
Abstract
During the last two decades, the importance of human genome copy number variation (CNV) in disease has become widely recognized. However, much is not understood about underlying mechanisms. We show how, although model organism research guides molecular understanding, important insights are gained from study of the wealth of information available in the clinic. We describe progress in explaining nonallelic homologous recombination (NAHR), a major cause of copy number change occurring when control of allelic recombination fails, highlight the growing importance of replicative mechanisms to explain complex events, and describe progress in understanding extreme chromosome reorganization (chromothripsis). Both nonhomologous end-joining and aberrant replication have significant roles in chromothripsis. As we study CNV, the processes underlying human genome evolution are revealed.
Collapse
|
38
|
Gamba BF, Vieira GH, Souza DH, Monteiro FF, Lorenzini JJ, Carvalho DR, Morreti-Ferreira D. Smith-Magenis syndrome: clinical evaluation in seven Brazilian patients. GENETICS AND MOLECULAR RESEARCH 2011; 10:2664-70. [PMID: 22057962 DOI: 10.4238/2011.october.31.17] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Smith-Magenis syndrome (SMS) is a complex congenital anomaly characterized by craniofacial anomalies, neurological and behavioral disorders. SMS is caused by a deletion in region 17p11.2, which includes the RAI1 gene (90% of cases), or by point mutation in the RAI1 gene (10% of cases). Laboratory diagnosis is through cytogenetic analysis by GTG banding and molecular cytogenetic analysis by FISH. We carried out an active search for patients in Associations of Parents and Friends of Exceptional Children (APAE) of São Paulo and genetic centers in Brazil. Forty-eight patients were screened for mental retardation, craniofacial abnormalities and stereotyped behavior with a diagnosis of SMS. In seven of them, chromosome banding at high resolution demonstrated chromosome 17p11.2 deletions, confirmed by FISH. We also made a meta-analysis of 165 cases reported between 1982 and 2010 to compare with the clinical data of our sample. We demonstrated differences between the frequencies of clinical signs among the cases reported and seven Brazilian cases of this study, such as dental anomalies, strabismus, ear infections, deep hoarse voice, hearing loss, and cardiac defects. Although the gold standard for diagnosis of SMS is FISH, we found that the GTG banding technique developed to evaluate chromosome 17 can be used for the SMS diagnosis in areas where the FISH technique is not available.
Collapse
Affiliation(s)
- B F Gamba
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, SP, Brasil
| | | | | | | | | | | | | |
Collapse
|
39
|
Velayati A, Knight MA, Stubblefield BK, Sidransky E, Tayebi N. Identification of recombinant alleles using quantitative real-time PCR implications for Gaucher disease. J Mol Diagn 2011; 13:401-5. [PMID: 21704274 DOI: 10.1016/j.jmoldx.2011.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/01/2011] [Accepted: 02/09/2011] [Indexed: 11/16/2022] Open
Abstract
Pseudogenes, resulting from duplications of functional genes, contribute to the functional complexity of their parental genes. The glucocerebrosidase gene (GBA), located in a gene-rich region on chromosome 1q 21, is mutated in Gaucher disease. The presence of contiguous, highly homologous pseudogenes for both GBA and metaxin 1 at this locus increases the likelihood of DNA rearrangement. We describe a facile method to identify and analyze recombinant alleles in patients with Gaucher disease. Genomic DNA from 20 patients with recombinant GBA alleles and five controls was evaluated to identify DNA rearrangements or copy number variation using six probes specific for either the GBA gene or pseudogene. Quantitative real-time PCR was performed on genomic DNA, and Southern blot analyses using HincII together with sequencing confirmed the real-time results. Both GBA fusions and duplications could be detected. Different sites of crossover were identified, and alleles resulting from gene conversion could be distinguished from reciprocal recombinant alleles. Quantitative real-time PCR is a sensitive and rapid method to detect fusions and duplications in patients with recombinant GBA alleles. This technique is more sensitive, faster, and cheaper than Southern blot analysis, and can be used in diagnostic laboratories, and to detect other recombinant alleles within the genome.
Collapse
Affiliation(s)
- Arash Velayati
- Section on Molecular Neurogenetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | | |
Collapse
|
40
|
Liu P, Lacaria M, Zhang F, Withers M, Hastings P, Lupski J. Frequency of nonallelic homologous recombination is correlated with length of homology: evidence that ectopic synapsis precedes ectopic crossing-over. Am J Hum Genet 2011; 89:580-8. [PMID: 21981782 DOI: 10.1016/j.ajhg.2011.09.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 10/16/2022] Open
Abstract
Genomic disorders constitute a class of diseases that are associated with DNA rearrangements resulting from region-specific genome instability, that is, genome architecture incites genome instability. Nonallelic homologous recombination (NAHR) or crossing-over in meiosis between sequences that are not in allelic positions (i.e., paralogous sequences) can result in recurrent deletions or duplications causing genomic disorders. Previous studies of NAHR have focused on description of the phenomenon, but it remains unclear how NAHR occurs during meiosis and what factors determine its frequency. Here we assembled two patient cohorts with reciprocal genomic disorders; deletion associated Smith-Magenis syndrome and duplication associated Potocki-Lupski syndrome. By assessing the full spectrum of rearrangement types from the two cohorts, we find that complex rearrangements (those with more than one breakpoint) are more prevalent in copy-number gains (17.7%) than in copy-number losses (2.3%); an observation that supports a role for replicative mechanisms in complex rearrangement formation. Interestingly, for NAHR-mediated recurrent rearrangements, we show that crossover frequency is positively associated with the flanking low-copy repeat (LCR) length and inversely influenced by the inter-LCR distance. To explain this, we propose that the probability of ectopic chromosome synapsis increases with increased LCR length, and that ectopic synapsis is a necessary precursor to ectopic crossing-over.
Collapse
|
41
|
Hirschfeldova K, Baxova A, Kebrdlova V, Solc R, Mihalova R, Lnenicka P, Vesela K, Stekrova J. Cryptic Chromosomal Rearrangements in Children with Idiopathic Mental Retardation in the Czech Population. Genet Test Mol Biomarkers 2011; 15:607-11. [DOI: 10.1089/gtmb.2010.0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Katerina Hirschfeldova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Alice Baxova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Vera Kebrdlova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Roman Solc
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Romana Mihalova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Petr Lnenicka
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Kamila Vesela
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Jitka Stekrova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| |
Collapse
|
42
|
Vilboux T, Ciccone C, Blancato JK, Cox GF, Deshpande C, Introne WJ, Gahl WA, Smith ACM, Huizing M. Molecular analysis of the Retinoic Acid Induced 1 gene (RAI1) in patients with suspected Smith-Magenis syndrome without the 17p11.2 deletion. PLoS One 2011; 6:e22861. [PMID: 21857958 PMCID: PMC3152558 DOI: 10.1371/journal.pone.0022861] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 06/30/2011] [Indexed: 11/28/2022] Open
Abstract
Smith-Magenis syndrome (SMS) is a complex neurobehavioral disorder characterized by multiple congenital anomalies. The syndrome is primarily ascribed to a ∼3.7 Mb de novo deletion on chromosome 17p11.2. Haploinsufficiency of multiple genes likely underlies the complex clinical phenotype. RAI1 (Retinoic Acid Induced 1) is recognized as a major gene involved in the SMS phenotype. Extensive genetic and clinical analyses of 36 patients with SMS-like features, but without the 17p11.2 microdeletion, yielded 10 patients with RAI1 variants, including 4 with de novo deleterious mutations, and 6 with novel missense variants, 5 of which were familial. Haplotype analysis showed two major RAI1 haplotypes in our primarily Caucasian cohort; the novel RAI1 variants did not occur in a preferred haplotype. RNA analysis revealed that RAI1 mRNA expression was significantly decreased in cells of patients with the common 17p11.2 deletion, as well as in those with de novo RAI1 variants. Expression levels varied in patients with familial RAI1 variants and in non-17p11.2 deleted patients without identified RAI1 defects. No correlation between SNP haplotype and RAI1 expression was found. Two clinical features, ocular abnormalities and polyembolokoilomania (object insertion), were significantly correlated with decreased RAI1 expression. While not significantly correlated, the presence of hearing loss, seizures, hoarse voice, childhood onset of obesity and specific behavioral aspects and the absence of immunologic abnormalities and cardiovascular or renal structural anomalies, appeared to be specific for the de novo RAI1 subgroup. Recognition of the combination of these features will assist in referral for RAI1 analysis of patients with SMS-like features without detectable microdeletion of 17p11.2. Moreover, RAI1 expression emerged as a genetic target for development of therapeutic interventions for SMS.
Collapse
Affiliation(s)
- Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Carla Ciccone
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jan K. Blancato
- Department of Oncology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Gerald F. Cox
- Division of Genetics, Department of Pediatrics, Harvard Medical School, Children's Hospital Boston, Boston, Massachusetts, United States of America
- Genzyme Corporation, Cambridge, Massachusetts, United States of America
| | - Charu Deshpande
- Department of Genetics, Guy's Hospital, London, United Kingdom
| | - Wendy J. Introne
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - William A. Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ann C. M. Smith
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marjan Huizing
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
43
|
Carmona-Mora P, Molina J, Encina CA, Walz K. Mouse models of genomic syndromes as tools for understanding the basis of complex traits: an example with the smith-magenis and the potocki-lupski syndromes. Curr Genomics 2011; 10:259-68. [PMID: 19949547 PMCID: PMC2709937 DOI: 10.2174/138920209788488508] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 04/07/2009] [Accepted: 04/09/2009] [Indexed: 11/29/2022] Open
Abstract
Each human's genome is distinguished by extra and missing DNA that can be “benign” or powerfully impact everything from development to disease. In the case of genomic disorders DNA rearrangements, such as deletions or duplications, correlate with a clinical specific phenotype. The clinical presentations of genomic disorders were thought to result from altered gene copy number of physically linked dosage sensitive genes. Genomic disorders are frequent diseases (~1 per 1,000 births). Smith-Magenis syndrome (SMS) and Potocki-Lupski syndrome (PTLS) are genomic disorders, associated with a deletion and a duplication, of 3.7 Mb respectively, within chromosome 17 band p11.2. This region includes 23 genes. Both syndromes have complex and distinctive phenotypes including multiple congenital and neurobehavioral abnormalities. Human chromosome 17p11.2 is syntenic to the 32-34 cM region of murine chromosome 11. The number and order of the genes are highly conserved. In this review, we will exemplify how genomic disorders can be modeled in mice and the advantages that such models can give in the study of genomic disorders in particular and gene copy number variation (CNV) in general. The contributions of the SMS and PTLS animal models in several aspects ranging from more specific ones, as the definition of the clinical aspects of the human clinical spectrum, the identification of dosage sensitive genes related to the human syndromes, to the more general contributions as the definition of genetic locus impacting obesity and behavior and the elucidation of general mechanisms related to the pathogenesis of gene CNV are discussed.
Collapse
|
44
|
Carmona-Mora P, Walz K. Retinoic Acid Induced 1, RAI1: A Dosage Sensitive Gene Related to Neurobehavioral Alterations Including Autistic Behavior. Curr Genomics 2011; 11:607-17. [PMID: 21629438 PMCID: PMC3078685 DOI: 10.2174/138920210793360952] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 10/08/2010] [Accepted: 10/21/2010] [Indexed: 12/15/2022] Open
Abstract
Genomic structural changes, such as gene Copy Number Variations (CNVs) are extremely abundant in the human genome. An enormous effort is currently ongoing to recognize and catalogue human CNVs and their associations with abnormal phenotypic outcomes. Recently, several reports related neuropsychiatric diseases (i.e. autism spectrum disorders, schizophrenia, mental retardation, behavioral problems, epilepsy) with specific CNV. Moreover, for some conditions, both the deletion and duplication of the same genomic segment are related to the phenotype. Syndromes associated with CNVs (microdeletion and microduplication) have long been known to display specific neurobehavioral traits. It is important to note that not every gene is susceptible to gene dosage changes and there are only a few dosage sensitive genes. Smith-Magenis (SMS) and Potocki-Lupski (PTLS) syndromes are associated with a reciprocal microdeletion and microduplication within chromosome 17p11.2. in humans. The dosage sensitive gene responsible for most phenotypes in SMS has been identified: the Retinoic Acid Induced 1 (RAI1). Studies on mouse models and humans suggest that RAI1 is likely the dosage sensitive gene responsible for clinical features in PTLS. In addition, the human RAI1 gene has been implicated in several neurobehavioral traits as spinocerebellar ataxia (SCA2), schizophrenia and non syndromic autism. In this review we discuss the evidence of RAI1 as a dosage sensitive gene, its relationship with different neurobehavioral traits, gene structure and mutations, and what is known about its molecular and cellular function, as a first step in the elucidation of the mechanisms that relate dosage sensitive genes with abnormal neurobehavioral outcomes.
Collapse
Affiliation(s)
- Paulina Carmona-Mora
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | | |
Collapse
|
45
|
Boone PM, Reiter RJ, Glaze DG, Tan DX, Lupski JR, Potocki L. Abnormal circadian rhythm of melatonin in Smith-Magenis syndrome patients with RAI1 point mutations. Am J Med Genet A 2011; 155A:2024-7. [PMID: 21739587 DOI: 10.1002/ajmg.a.34098] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 04/13/2011] [Indexed: 12/15/2022]
Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | | | | | | | | |
Collapse
|
46
|
Pao PC, Huang NK, Liu YW, Yeh SH, Lin ST, Hsieh CP, Huang AM, Huang HS, Tseng JT, Chang WC, Lee YC. A novel RING finger protein, Znf179, modulates cell cycle exit and neuronal differentiation of P19 embryonal carcinoma cells. Cell Death Differ 2011; 18:1791-804. [PMID: 21566658 PMCID: PMC3190115 DOI: 10.1038/cdd.2011.52] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Znf179 is a member of the RING finger protein family. During embryogenesis, Znf179 is expressed in a restricted manner in the brain, suggesting a potential role in nervous system development. In this report, we show that the expression of Znf179 is upregulated during P19 cell neuronal differentiation. Inhibition of Znf179 expression by RNA interference significantly attenuated neuronal differentiation of P19 cells and a primary culture of cerebellar granule cells. Using a microarray approach and subsequent functional annotation analysis, we identified differentially expressed genes in Znf179-knockdown cells and found that several genes are involved in development, cellular growth, and cell cycle control. Flow cytometric analyses revealed that the population of G0/G1 cells decreased in Znf179-knockdown cells. In agreement with the flow cytometric data, the number of BrdU-incorporated cells significantly increased in Znf179-knockdown cells. Moreover, in Znf179-knockdown cells, p35, a neuronal-specific Cdk5 activator that is known to activate Cdk5 and may affect the cell cycle, and p27, a cell cycle inhibitor, also decreased. Collectively, these results show that induction of the Znf179 gene may be associated with p35 expression and p27 protein accumulation, which lead to cell cycle arrest in the G0/G1 phase, and is critical for neuronal differentiation of P19 cells.
Collapse
Affiliation(s)
- P-C Pao
- Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Smith–Magenis syndrome: haploinsufficiency of RAI1 results in altered gene regulation in neurological and metabolic pathways. Expert Rev Mol Med 2011; 13:e14. [DOI: 10.1017/s1462399411001827] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Smith–Magenis syndrome (SMS) is a complex neurobehavioural disorder characterised by intellectual disability, self-injurious behaviours, sleep disturbance, obesity, and craniofacial and skeletal anomalies. Diagnostic strategies are focused towards identification of a 17p11.2 microdeletion encompassing the gene RAI1 (retinoic acid induced 1) or a mutation of RAI1. Molecular evidence shows that most SMS features are due to RAI1 haploinsufficiency, whereas variability and severity are modified by other genes in the 17p11.2 region for 17p11.2 deletion cases. The functional role of RAI1 is not completely understood, but it is probably a transcription factor acting in several different biological pathways that are dysregulated in SMS. Functional studies based on the hypothesis that RAI1 acts through phenotype-specific pathways involving several downstream genes have shown that RAI1 gene dosage is crucial for normal regulation of circadian rhythm, lipid metabolism and neurotransmitter function. Here, we review the clinical and molecular features of SMS and explore more recent studies supporting possible therapeutic strategies for behavioural management.
Collapse
|
48
|
Soler-Alfonso C, Motil KJ, Turk CL, Robbins-Furman P, Friedman EM, Zhang F, Lupski JR, Fraley JK, Potocki L. Potocki-Lupski syndrome: a microduplication syndrome associated with oropharyngeal dysphagia and failure to thrive. J Pediatr 2011; 158:655-659.e2. [PMID: 21168152 PMCID: PMC3059370 DOI: 10.1016/j.jpeds.2010.09.062] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 08/23/2010] [Accepted: 09/22/2010] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Failure to thrive (FTT) is a feature of children with Potocki-Lupski syndrome (PTLS) [duplication 17p11.2]. This study was designed to describe the growth characteristics of 24 subjects with PTLS from birth through age 5 years in conjunction with relevant physical features and swallow function studies. STUDY DESIGN We evaluated 24 individuals with PTLS who were ascertained by chromosome analysis and/or array comparative genome hybridization. Clinical assessments included review of medical records, physical examination, otolaryngological examination, and swallow function studies. Measures of height and weight were converted to Z-scores. RESULTS The mean weight-for-age and weight-for-length Z-scores at birth were lower (P < .01) than the reference standard and did not change with age. A history of poor feeding, hypotonia, and FTT were reported in 92%, 88%, and 71%, respectively. Individuals with hypotonia had lower weight-for-age and body mass index-for-age Z-scores (P = .01). Swallow function studies demonstrated at least one abnormality in all subjects. CONCLUSIONS FTT is common in children with PTLS. We hypothesize that oropharyngeal dysphagia and hypotonia likely contribute to FTT in patients with PTLS and recommend that once a diagnosis is established, the individual be assessed for feeding and growth issues and be availed of oromotor therapy and nutritional services.
Collapse
Affiliation(s)
- Claudia Soler-Alfonso
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Wang Y, Yau YY, Perkins-Balding D, Thomson JG. Recombinase technology: applications and possibilities. PLANT CELL REPORTS 2011; 30:267-85. [PMID: 20972794 PMCID: PMC3036822 DOI: 10.1007/s00299-010-0938-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/08/2010] [Indexed: 05/02/2023]
Abstract
The use of recombinases for genomic engineering is no longer a new technology. In fact, this technology has entered its third decade since the initial discovery that recombinases function in heterologous systems (Sauer in Mol Cell Biol 7(6):2087-2096, 1987). The random insertion of a transgene into a plant genome by traditional methods generates unpredictable expression patterns. This feature of transgenesis makes screening for functional lines with predictable expression labor intensive and time consuming. Furthermore, an antibiotic resistance gene is often left in the final product and the potential escape of such resistance markers into the environment and their potential consumption raises consumer concern. The use of site-specific recombination technology in plant genome manipulation has been demonstrated to effectively resolve complex transgene insertions to single copy, remove unwanted DNA, and precisely insert DNA into known genomic target sites. Recombinases have also been demonstrated capable of site-specific recombination within non-nuclear targets, such as the plastid genome of tobacco. Here, we review multiple uses of site-specific recombination and their application toward plant genomic engineering. We also provide alternative strategies for the combined use of multiple site-specific recombinase systems for genome engineering to precisely insert transgenes into a pre-determined locus, and removal of unwanted selectable marker genes.
Collapse
Affiliation(s)
- Yueju Wang
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
| | - Yuan-Yeu Yau
- Department of Plant and Microbial Biology, Plant Gene Expression Center, USDA-ARS, University of California-Berkeley, 800 Buchanan St., Albany, CA 94710 USA
| | | | - James G. Thomson
- Crop Improvement and Utilization Unit, USDA-ARS WRRC, 800 Buchanan St., Albany, CA 94710 USA
| |
Collapse
|
50
|
Yusupov R, Roberts AE, Lacro RV, Sandstrom M, Ligon AH. Potocki-Lupski syndrome: An inherited dup(17)(p11.2p11.2) with hypoplastic left heart. Am J Med Genet A 2011; 155A:367-71. [DOI: 10.1002/ajmg.a.33845] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|