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Yuan X, Chen L, Saffen D. Allele-Specific Regulation of the Candidate Autism Liability Gene RAI1 by the Enhancer Variant rs4925102 ( C/G). Genes (Basel) 2024; 15:460. [PMID: 38674394 PMCID: PMC11049881 DOI: 10.3390/genes15040460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
Retinoic acid-induced 1 (RAI1) is a dosage-sensitive gene that causes autistic phenotypes when deleted or duplicated. Observations from clinical cases and animal models also suggest that changes of RAI1 expression levels contribute to autism. Previously, we used a bioinformatic approach to identify several single nucleotide polymorphisms (SNPs) located within the 5'-region of RAI1 that correlate with RAI1 mRNA expression in the human brain. In particular, the SNP rs4925102 was identified as a candidate cis-acting regulatory variant, the genotype of which may affect the binding of transcription factors that influence RAI1 mRNA expression. In this study, we provide experimental evidence based on reporter gene, chromatin immunoprecipitation (ChIP), and chromatin conformation capture (3C) assays that rs4925102 regulates RAI1 mRNA expression in an allele-specific manner in human cell lines, including the neuroblastoma-derived cell line SH-SY5Y. We also describe a statistically significant association between rs4925102 genotype and autism spectrum disorder (ASD) diagnosis in a case-control study and near-statistically significant association in an Autism Genome Project (AGP) transmission disequilibrium (TDT) study using Caucasian subjects.
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Affiliation(s)
- Xi Yuan
- Institutes of Brain Science, Fudan University, Shanghai 200032, China;
| | - Li Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - David Saffen
- Institutes of Brain Science, Fudan University, Shanghai 200032, China;
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200032, China
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2
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Chang YT, Lee YJ, Haque M, Chang HC, Javed S, Lin YC, Cho Y, Abramovitz J, Chin G, Khamis A, Raja R, Murai KK, Huang WH. Comparative analyses of the Smith-Magenis syndrome protein RAI1 in mice and common marmoset monkeys. J Comp Neurol 2024; 532:e25589. [PMID: 38289192 DOI: 10.1002/cne.25589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/11/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Retinoic acid-induced 1 (RAI1) encodes a transcriptional regulator critical for brain development and function. RAI1 haploinsufficiency in humans causes a syndromic autism spectrum disorder known as Smith-Magenis syndrome (SMS). The neuroanatomical distribution of RAI1 has not been quantitatively analyzed during the development of the prefrontal cortex, a brain region critical for cognitive function and social behaviors and commonly implicated in autism spectrum disorders, including SMS. Here, we performed comparative analyses to uncover the evolutionarily convergent and divergent expression profiles of RAI1 in major cell types during prefrontal cortex maturation in common marmoset monkeys (Callithrix jacchus) and mice (Mus musculus). We found that while RAI1 in both species is enriched in neurons, the percentage of excitatory neurons that express RAI1 is higher in newborn mice than in newborn marmosets. By contrast, RAI1 shows similar neural distribution in adult marmosets and adult mice. In marmosets, RAI1 is expressed in several primate-specific cell types, including intralaminar astrocytes and MEIS2-expressing prefrontal GABAergic neurons. At the molecular level, we discovered that RAI1 forms a protein complex with transcription factor 20 (TCF20), PHD finger protein 14 (PHF14), and high mobility group 20A (HMG20A) in the marmoset brain. In vitro assays in human cells revealed that TCF20 regulates RAI1 protein abundance. This work demonstrates that RAI1 expression and protein interactions are largely conserved but with some unique expression in primate-specific cells. The results also suggest that altered RAI1 abundance could contribute to disease features in disorders caused by TCF20 dosage imbalance.
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Affiliation(s)
- Ya-Ting Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu-Ju Lee
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Minza Haque
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Hao-Cheng Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sehrish Javed
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu Cheng Lin
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yoobin Cho
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Joseph Abramovitz
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Gabriella Chin
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Asma Khamis
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Reesha Raja
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Keith K Murai
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Wei-Hsiang Huang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
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3
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Talantseva OI, Portnova GV, Romanova RS, Martynova DA, Sysoeva OV, Grigorenko EL. Does the Potocki–Lupski Syndrome Convey the Autism Spectrum Disorder Phenotype? Case Report and Scoping Review. J Pers Med 2023; 13:jpm13030439. [PMID: 36983620 PMCID: PMC10053863 DOI: 10.3390/jpm13030439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Potocki–Lupski Syndrome (PTLS) is a rare condition associated with a duplication of 17p11.2 that may underlie a wide range of congenital abnormalities and heterogeneous behavioral phenotypes. Along with developmental delay and intellectual disability, autism-specific traits are often reported to be the most common among patients with PTLS. To contribute to the discussion of the role of autism spectrum disorder (ASD) in the PTLS phenotype, we present a case of a female adolescent with a de novo dup(17) (p11.2p11.2) without ASD features, focusing on in-depth clinical, behavioral, and electrophysiological (EEG) evaluations. Among EEG features, we found the atypical peak–slow wave patterns and a unique saw-like sharp wave of 13 Hz that was not previously described in any other patient. The power spectral density of the resting state EEG was typical in our patient with only the values of non-linear EEG dynamics: Hjorth complexity and fractal dimension were drastically attenuated compared with the patient’s neurotypical peers. Here we also summarize results from previously published reports of PTLS that point to the approximately 21% occurrence of ASD in PTLS that might be biased, taking into account methodological limitations. More consistent among PTLS patients were intellectual disability and speech and language disorders.
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Affiliation(s)
- Oksana I. Talantseva
- Center for Cognitive Sciences, Sirius University of Science and Technology, 354340 Sirius, Russia
| | - Galina V. Portnova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
| | - Raisa S. Romanova
- Center for Cognitive Sciences, Sirius University of Science and Technology, 354340 Sirius, Russia
| | - Daria A. Martynova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
| | - Olga V. Sysoeva
- Center for Cognitive Sciences, Sirius University of Science and Technology, 354340 Sirius, Russia
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
| | - Elena L. Grigorenko
- Center for Cognitive Sciences, Sirius University of Science and Technology, 354340 Sirius, Russia
- Department of Psychology, University of Houston, Houston, TX 77204, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Child Study Center, Yale University, New Haven, CT 06519, USA
- Correspondence:
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4
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Schneeweiss MR, Dale B, Ejaz R. Diagnosis and clinical presentation of two individuals with a rare TCF20 pathogenic variant. BMJ Case Rep 2022; 15:15/12/e248995. [PMID: 36593604 PMCID: PMC9730367 DOI: 10.1136/bcr-2022-248995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
TCF20-associated neurodevelopmental disorder (TAND) is a rare and phenotypically variable genetic condition. Common features include intellectual disability, neurobehavioural concerns, postnatal tall stature and hypotonia.Two unrelated early adolescent males were referred to genetics for assessment of developmental delay. The first male of Caucasian descent had a history of autism spectrum disorder (ASD), mitral valve prolapse and subtle craniofacial dysmorphisms. The second male of Somali descent had a history of intellectual disability, thick corpus callosum and ASD. Whole-exome sequencing revealed a pathogenic variant in TCF20 in both individuals. Further testing revealed that the former individual's mother was mosaic for the TCF20 pathogenic variant.We report two individuals with TCF20 pathogenic variants presenting with unique findings, including thick corpus callosum, family history of mosaicism and cardiac anomalies. These examples expand the TAND phenotype, describe associated dysmorphism in a minority group and highlight the importance of rare disease research.
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Affiliation(s)
| | - Breanne Dale
- Genetics and Metabolics Clinic, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada .,Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
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5
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Chang HC, Lee YJ, Javed S, Haque M, Chang YT, Lin YC, Oram C, Huang WH. rAAV-CRISPRa therapy corrects Rai1 haploinsufficiency and rescues selective disease features in Smith-Magenis syndrome mice. J Biol Chem 2022; 299:102728. [PMID: 36410433 PMCID: PMC9762195 DOI: 10.1016/j.jbc.2022.102728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/20/2022] Open
Abstract
Haploinsufficiency in retinoic acid induced 1 (RAI1) causes Smith-Magenis syndrome (SMS), a severe neurodevelopmental disorder characterized by neurocognitive deficits and obesity. Currently, curative treatments for SMS do not exist. Here, we take a recombinant adeno-associated virus (rAAV)-clustered regularly interspaced short palindromic repeats activation (CRISPRa) approach to increase expression of the remaining intact Rai1 allele. Building upon our previous work that found the paraventricular nucleus of hypothalamus plays a central role in SMS pathogenesis, we performed paraventricular nucleus of hypothalamus-specific rAAV-CRISPRa therapy by increasing endogenous Rai1 expression in SMS (Rai1±) mice. We found that rAAV-CRISPRa therapy rescues excessive repetitive behavior, delays the onset of obesity, and partially reduces hyperphagia in SMS mice. Our work provides evidence that rAAV-CRISPRa therapy during early adolescence can boost the expression of healthy Rai1 allele and modify disease progression in a mouse model of Smith-Magenis syndrome.
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Affiliation(s)
- Hao-Cheng Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu-Ju Lee
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sehrish Javed
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Minza Haque
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Ya-Ting Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu Cheng Lin
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Cameron Oram
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Wei-Hsiang Huang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada,For correspondence: Wei-Hsiang Huang
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6
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Sironi A, Bestetti I, Masciadri M, Tumiatti F, Crippa M, Pantaleoni C, Russo S, D'Arrigo S, Milani D, Larizza L, Finelli P. A unique Smith-Magenis patient with a de novo intragenic deletion on the maternally inherited overexpressed RAI1 allele. Eur J Hum Genet 2022; 30:1233-8. [PMID: 35821519 DOI: 10.1038/s41431-022-01143-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [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.
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7
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Musabi M, Saker A, Baer J, Wang P, Mohseni Meybodi A, Prasad C, Bhattacharya S. Road to a rare diagnosis: Description of novel unbalanced translocation causing partial trisomy 17p. Clin Case Rep 2022; 10:e6343. [PMID: 36237944 PMCID: PMC9536500 DOI: 10.1002/ccr3.6343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/17/2022] [Accepted: 08/31/2022] [Indexed: 11/11/2022] Open
Abstract
Trisomy 17 is a rare chromosomal disorder. Existing literature on the topic is limited and mostly refer to mosaic Trisomy 17 cases. Our report summarizes the 70‐day clinical course of a late preterm neonate with partial Trisomy 17p karyotype 46,XY,der(14)t(14;17)(p11.1;p11.2) dpat. Trisomy 17 due to unbalanced translocation is rare, and our case elaborates the clinical presentation with intestinal malfunction without any anatomical pathology and urethral diverticulum and the ethical dilemma in decision‐making. The male proband was born at 35 weeks with antenatal findings of multiple neurological and other abnormalities such as cystic hygroma, absent corpus collosum, high riding third ventricle, absent cavum septum pellucidum, indented occiput, absent ductus venous, and intrauterine growth restriction. The postnatal findings included significant facial dysmorphisms with short palpebral fissures, hypertelorism, low set ears, micrognathia, hirsutism, and single palmar creases, central hypotonia, and hyperreflexia of upper limbs bilaterally. Genital‐urinary assessment revealed a urinary diverticulum and significantly underdeveloped scrotum with undescended testes. Infant had excessive irritability and resistance to sleep despite increasing doses of analgesia and sedation, and persistent respiratory and feeding difficulties. Enteral nutrition could not be established due to profuse and persistent diarrhea, necessitating use of total parenteral nutrition. Microarray assay exhibited a pathogenic copy number gain of approximately 21.4 Mb of chromosome region 17p13.3p11.2. Follow‐up chromosome analysis and FISH revealed an abnormal male karyotype with a derivative chromosome 14, resulting from an unbalanced translocation between the short arm of one chromosome 14 and the short arm of one chromosome 17, effectively resulting in trisomy 17p11.2. It was derived from a paternal balanced t(14;17)(p11.1;p11.2) as shown by chromosome analysis and FISH studies. The rarity of this chromosomal disorder contributed to difficulty with prognosis and led to bioethical dilemma regarding life‐sustaining measures and quality of life. Through shared decision‐making processes and in consideration of poor prognosis, parents decided to withdraw life‐sustaining care and the proband died at postnatal day of life 70.
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Affiliation(s)
- Melab Musabi
- Department of Paediatrics, Neonatal‐ Perinatal MedicineWestern University London OntarioLondonOntarioCanada
| | - Ayman Saker
- Department of Paediatrics, Neonatal‐ Perinatal MedicineWestern University London OntarioLondonOntarioCanada
| | - Jessi Baer
- Department of Paediatrics, Neonatal‐ Perinatal MedicineWestern University London OntarioLondonOntarioCanada
| | - Peter Wang
- Department of Paediatrics, Pediatric SurgeryWestern UniversityLondonOntarioCanada
| | - Anahita Mohseni Meybodi
- Department of Pathology and Laboratory Medicine Western UniversityLondonOntarioCanada,Molecular Diagnostics DivisionLondon Health Sciences CentreLondonOntarioCanada
| | - Chitra Prasad
- Department of Paediatrics, Section of Genetics and MetabolismWestern University London OntarioLondonOntarioCanada
| | - Soume Bhattacharya
- Department of Paediatrics, Neonatal‐ Perinatal MedicineWestern University London OntarioLondonOntarioCanada
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8
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Javed S, Lee YJ, Xu J, Huang WH. Temporal dissection of Rai1 function reveals brain-derived neurotrophic factor as a potential therapeutic target for Smith-Magenis syndrome. Hum Mol Genet 2021; 31:275-288. [PMID: 34463714 DOI: 10.1093/hmg/ddab245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/02/2021] [Accepted: 08/20/2021] [Indexed: 12/17/2022] Open
Abstract
Haploinsufficiency of RAI1 is responsible for Smith-Magenis Syndrome (SMS), a childhood neurodevelopmental disorder associated with hyperphagia, obesity, and autistic features. We previously showed that constitutive inactivation of one or both copies of Rai1 in the germline or developing brain induces SMS-like neurobehavioral deficits and obesity in mice. By contrast, the postnatal function of Rai1 is unclear. Here, we globally deleted one or both copies of Rai1 during two postnatal developmental windows by generating an inducible Rai1 knockout mouse model. We found that delayed Rai1 deletion at 3 or 8 weeks of age had no effect on neurobehavioral functions but resulted in adult-onset obesity and decreased expression of brain-derived neurotrophic factor (Bdnf) in the hypothalamus. Remarkably, genetic overexpression of human Bdnf in Rai1 heterozygous mice reversed SMS-like obesity, hyperphagia, metabolic syndrome-like features, and hyposociability. Increasing Bdnf signaling in the paraventricular nucleus of the hypothalamus (PVH) or the ventromedial nucleus of the hypothalamus (VMH) was sufficient to mediate the anti-obesity effect. Our work identifies the function of Rai1 in different temporal windows after birth and provides in vivo evidence that increasing Bdnf signaling is therapeutically effective in a preclinical mouse model of SMS.
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Affiliation(s)
- Sehrish Javed
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, McGill University, Québec H3G 1A3, Canada.,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec H3G 1A3, Canada
| | - Yu-Ju Lee
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, McGill University, Québec H3G 1A3, Canada.,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec H3G 1A3, Canada
| | - Jin Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei-Hsiang Huang
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, McGill University, Québec H3G 1A3, Canada.,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec H3G 1A3, Canada
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9
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Franciskovich R, Soler-Alfonso C, Neira-Fresneda J, Lupski JR, McCann-Crosby B, Potocki L. Short stature and growth hormone deficiency in a subset of patients with Potocki-Lupski syndrome: Expanding the phenotype of PTLS. Am J Med Genet A 2020; 182:2077-2084. [PMID: 32656927 PMCID: PMC8445515 DOI: 10.1002/ajmg.a.61741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 11/07/2022]
Abstract
Potocki-Lupski Syndrome (PTLS, MIM 610883), or duplication of chromosome 17p11.2, is a clinically recognizable condition characterized by infantile hypotonia, failure to thrive, developmental delay, intellectual disability, and congenital anomalies. Short stature, classified as greater than two standard deviations below the mean, has not previously been considered a major feature of PTLS. Retrospective chart review on a cohort of 37 individuals with PTLS was performed to investigate the etiology of short stature. Relevant data included anthropometric measurements, insulin growth factor-1 (IGF-1), insulin-like growth factor binding protein 3 (IGFBP-3), growth hormone (GH) stimulation testing, blood glucose levels, brain MRI, and bone age. Approximately 25% (9/37) of individuals with PTLS had short stature. Growth hormone deficiency (GHD) was definitively identified in two individuals. These two PTLS patients with growth hormone deficiency, as well as three others with short stature and no documented GHD, received growth hormone and obtained improvement in linear growth. One individual was identified to have pituitary abnormalities on MRI and had complications of hypoglycemia due to unrecognized GHD. Individuals with PTLS can benefit from undergoing evaluation for GHD should they present with short stature or hypoglycemia. Early identification of GHD could facilitate potential therapeutic benefit for individuals with PTLS, including linear growth, musculoskeletal, and in cases of hypoglycemia, potentially cognitive development as well.
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Affiliation(s)
- Rachel Franciskovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, USA
| | - Claudia Soler-Alfonso
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, USA
| | | | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Bonnie McCann-Crosby
- Texas Children’s Hospital, Houston, USA
- Division of Pediatric Endocrinology, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, USA
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10
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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: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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11
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Ciaccio C, Pantaleoni C, Milani D, Alfei E, Sciacca FL, Canafoglia L, Erbetta A, D'Arrigo S. Neurological phenotype of Potocki-Lupski syndrome. Am J Med Genet A 2020; 182:2317-2324. [PMID: 33043631 DOI: 10.1002/ajmg.a.61789] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/19/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022]
Abstract
Potocki-Lupski syndrome is a condition mainly characterized by infantile hypotonia, developmental delay/intellectual disability (DD/ID), and congenital anomalies, caused by duplications of the 17p11.2 region, encompassing RAI1 gene. Its clinical presentation is extremely variable, especially for what concerns the cognitive level and the behavioral phenotype. Such aspects, as well as the dysmorphic/malformative ones, have been covered by previous studies; otherwise neurological features have never been systematically described. In order to delineate the neurological phenotype of Potocki-Lupski Syndrome, we collect an 8-patients cohort. Developmental milestones are delayed and a mild to moderate cognitive impairment is present in all patients, variably associated with features of autism spectrum disorder, behavioral disturb, and sleep disturb. Hypotonia appears a less frequent finding than what previously reported, while motor clumsiness/coordination impairment is frequent. EGG registration demonstrated a common pattern with excess of diffuse rhythmic activity in sleep phases or while the patient is falling asleep. Brain MRI did not reveal common anomalies, although unspecific white matter changes may be present. We discuss such findings and compare them to literature data, offering an overview on the neurological and cognitive-behavioral presentation of the syndrome.
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Affiliation(s)
- Claudia Ciaccio
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatria Alta Intensità di Cura, Milan, Italy
| | - Enrico Alfei
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Pediatric Neurology Unit-Vittore Buzzi Children's Hospital-ASST Fatebenefratelli-Sacco, Milan, Italy
| | - Francesca L Sciacca
- Laboratory of Cytogenetic, Neurological Biochemistry and Neuropharmacology Unit, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Canafoglia
- Neurophysiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alessandra Erbetta
- Department of Neuroradiology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefano D'Arrigo
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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12
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Morales Z, Martin-Lepe G. Intervención en Atención Temprana en un caso de Potocki-Lupski. Clínica Contemporánea 2020. [DOI: 10.5093/cc2020a11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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Missig G, McDougle CJ, Carlezon WA. Sleep as a translationally-relevant endpoint in studies of autism spectrum disorder (ASD). Neuropsychopharmacology 2020; 45:90-103. [PMID: 31060044 PMCID: PMC6879602 DOI: 10.1038/s41386-019-0409-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
Abstract
Sleep has numerous advantages for aligning clinical and preclinical (basic neuroscience) studies of neuropsychiatric illness. Sleep has high translational relevance, because the same endpoints can be studied in humans and laboratory animals. In addition, sleep experiments are conducive to continuous data collection over long periods (hours/days/weeks) and can be based on highly objective neurophysiological measures. Here, we provide a translationally-oriented review on what is currently known about sleep in the context of autism spectrum disorder (ASD), including ASD-related conditions, thought to have genetic, environmental, or mixed etiologies. In humans, ASD is frequently associated with comorbid medical conditions including sleep disorders. Animal models used in the study of ASD frequently recapitulate dysregulation of sleep and biological (diurnal, circadian) rhythms, suggesting common pathophysiologies across species. As our understanding of the neurobiology of ASD and sleep each become more refined, it is conceivable that sleep-derived metrics may offer more powerful biomarkers of altered neurophysiology in ASD than the behavioral tests currently used in humans or lab animals. As such, the study of sleep in animal models for ASD may enable fundamentally new insights on the condition and represent a basis for strategies that enable the development of more effective therapeutics.
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Affiliation(s)
- Galen Missig
- 0000 0000 8795 072Xgrid.240206.2Basic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA USA
| | - Christopher J. McDougle
- 0000 0004 0386 9924grid.32224.35Lurie Center for Autism, Massachusetts General Hospital, Lexington, MA USA ,000000041936754Xgrid.38142.3cDepartment of Psychiatry, Harvard Medical School, Boston, MA USA
| | - William A. Carlezon
- 0000 0000 8795 072Xgrid.240206.2Basic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA USA
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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15
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Varon A, Whitt Z, Kalika PM, Potocki L, Barbouth DS, Walz K. Arnold‐Chiari type 1 malformation in Potocki–Lupski syndrome. Am J Med Genet A 2019; 179:1366-1370. [DOI: 10.1002/ajmg.a.61187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Alberto Varon
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of MedicineUniversity of Miami Miami Florida
| | - Zachary Whitt
- Medical College of Georgia, Augusta University Augusta Georgia
| | - Paige M. Kalika
- Department of Neurology, Miller School of MedicineUniversity of Miami Miami Florida
| | - Lorraine Potocki
- Department of Molecular and Human Genetics Baylor College of MedicineTexas Children's Hospital Houston Texas
| | - Deborah S. Barbouth
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of MedicineUniversity of Miami Miami Florida
| | - Katherina Walz
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of MedicineUniversity of Miami Miami Florida
- John P. Hussman Institute for Human Genomics, University of Miami Miami Florida
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16
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Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KM, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Al Shamsi A, Fanning EA, Wierenga KJ, Scott DA, Ben-Neriah Z, Meiner V, Cassuto H, Elpeleg O, Holder JL, Burrage LC, Seaver LH, Van Maldergem L, Mahida S, Soul JS, Marlatt M, Matyakhina L, Vogt J, Gold JA, Park SM, Varghese V, Lampe AK, Kumar A, Lees M, Holder-Espinasse M, McConnell V, Bernhard B, Blair E, Harrison V, Muzny DM, Gibbs RA, Elsea SH, Posey JE, Bi W, Lalani S, Xia F, Yang Y, Eng CM, Lupski JR, Liu P. De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. Genome Med 2019; 11:12. [PMID: 30819258 PMCID: PMC6393995 DOI: 10.1186/s13073-019-0623-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith-Magenis syndrome (deletion/haploinsufficiency) and Potocki-Lupski syndrome (duplication/triplosensitivity). METHODS Genome-wide analyses by exome sequencing (ES) and chromosomal microarray analysis (CMA) identified individuals with heterozygous, likely damaging, loss-of-function alleles in TCF20. We implemented further molecular and clinical analyses to determine the inheritance of the pathogenic variant alleles and studied the spectrum of phenotypes. RESULTS We report 25 unique inactivating single nucleotide variants/indels (1 missense, 1 canonical splice-site variant, 18 frameshift, and 5 nonsense) and 4 deletions of TCF20. The pathogenic variants were detected in 32 patients and 4 affected parents from 31 unrelated families. Among cases with available parental samples, the variants were de novo in 20 instances and inherited from 4 symptomatic parents in 5, including in one set of monozygotic twins. Two pathogenic loss-of-function variants were recurrent in unrelated families. Patients presented with a phenotype characterized by developmental delay, intellectual disability, hypotonia, variable dysmorphic features, movement disorders, and sleep disturbances. CONCLUSIONS TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith-Magenis syndrome. Together with previously described cases, the clinical entity of TCF20-associated neurodevelopmental disorders (TAND) emerges from a genotype-driven perspective.
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Affiliation(s)
- Francesco Vetrini
- Baylor Genetics, Houston, TX, 77021, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mohnish Suri
- Nottingham Genetics Service, Nottingham City Hospital, Nottingham, UK
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberly Margaret Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Rebecca O Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Sue Holder
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | | | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jill M Harris
- Dell Children's Medical Group, Austin, TX, 78723, USA
| | | | - Matthew Pastore
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Kim L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Makanko Komara
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | | | - Elizabeth A Fanning
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Present address: Mayo Clinic Florida, Department of Clinical Genomics, Jacksonville, FL, 32224, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ziva Ben-Neriah
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, 91120, Jerusalem, Israel
| | - J Lloyd Holder
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurie H Seaver
- Department of Pediatrics, University of Hawaii, Honolulu, HI, 96826, USA
| | | | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Janet S Soul
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Margaret Marlatt
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | | | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners; and Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - June-Anne Gold
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Soo-Mi Park
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Vinod Varghese
- All-Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - Anne K Lampe
- South East of Scotland Clinical Genetic Service, Western General Hospital, Edinburgh, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | | | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Birgitta Bernhard
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | - Ed Blair
- Oxford Regional Genetics Service, Oxford University Hospitals, Oxford, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | | | - Donna M Muzny
- 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
| | - 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
| | - Sarah H Elsea
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Weimin Bi
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema Lalani
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Baylor Genetics, Houston, TX, 77021, USA.,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, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Pengfei Liu
- Baylor Genetics, Houston, TX, 77021, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Huang WH, Wang DC, Allen WE, Klope M, Hu H, Shamloo M, Luo L. Early adolescent Rai1 reactivation reverses transcriptional and social interaction deficits in a mouse model of Smith-Magenis syndrome. Proc Natl Acad Sci U S A 2018; 115:10744-9. [PMID: 30275311 DOI: 10.1073/pnas.1806796115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Losing one copy of the RAI1 gene causes Smith–Magenis syndrome (SMS), a neurodevelopmental disorder. Using a newly generated SMS mouse model, this study demonstrates that restoring the Rai1 gene dose in an early postnatal window could repair gene expression and social interaction deficits in this SMS model. The SMS mouse model also showed a reduced density of dendritic spines, anatomical correlates of excitatory synapses, in the prefrontal cortex. Artificial activation of prefrontal cortex neurons partially alleviated the behavioral deficits. These findings suggest that, similar to Rett syndrome, SMS is caused by disruption of a chromatin-modifying gene with reversible developmental phenotypes, highlighting the potential treatment windows in childhood or adolescence. Haploinsufficiency of Retinoic Acid Induced 1 (RAI1) causes Smith–Magenis syndrome (SMS), a syndromic autism spectrum disorder associated with craniofacial abnormalities, intellectual disability, and behavioral problems. There is currently no cure for SMS. Here, we generated a genetic mouse model to determine the reversibility of SMS-like neurobehavioral phenotypes in Rai1 heterozygous mice. We show that normalizing the Rai1 level 3–4 wk after birth corrected the expression of genes related to neural developmental pathways and fully reversed a social interaction deficit caused by Rai1 haploinsufficiency. In contrast, Rai1 reactivation 7–8 wk after birth was not beneficial. We also demonstrated that the correct Rai1 dose is required in both excitatory and inhibitory neurons for proper social interactions. Finally, we found that Rai1 heterozygous mice exhibited a reduction of dendritic spines in the medial prefrontal cortex (mPFC) and that optogenetic activation of mPFC neurons in adults improved the social interaction deficit of Rai1 heterozygous mice. Together, these results suggest the existence of a postnatal temporal window during which restoring Rai1 can improve the transcriptional and social behavioral deficits in a mouse model of SMS. It is possible that circuit-level interventions would be beneficial beyond this critical window.
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18
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Tesner P, Vlckova M, Drabova J, Vseticka J, Klimova A, Lastuvkova J, Zidovska J, Kremlikova Pourova R, Hancarova M, Sedlacek Z, Kocarek E. Molecular Cytogenetic Diagnostics of Marker Chromosomes: Analysis in Four Prenatal Cases and Long-Term Clinical Evaluation of Carriers. Cytogenet Genome Res 2018; 154:187-195. [DOI: 10.1159/000488790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2018] [Indexed: 01/15/2023] Open
Abstract
The prenatal finding of a small supernumerary marker chromosome (sSMC) is a challenge for genetic counseling. Our analytic algorithm is based on sSMC frequencies and multicolor FISH to accelerate the procedure. The chromosomal origin, size, and degree of mosaicism of the sSMC then determine the prognosis. We illustrate the effectiveness on 4 prenatally identified de novo mosaic sSMCs derived from chromosomes 13/21, X, 3, and 17. Three sSMC carriers had a good prognosis and apparently healthy children were born, showing no abnormality till the last examination at the age of 4 years. One case had a poor prognosis, and the parents decided to terminate the pregnancy. Our work contributes to the laboratory and clinical management of prenatally detected sSMCs. FISH is a reliable method for fast sSMC evaluation and prognosis assessment; it prevents unnecessary delays and uncertainty, allows informed decision making, and reduces unnecessary pregnancy terminations.
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Abstract
This review summarizes common microdeletion and microduplication syndromes and highlights important updates in patient-care needs for people with these conditions (22q11.2, 7q11.23, 17p11.2, and 16p11.2). These conditions are in chromosomal "hotspots" and have an estimated prevalence of 1 in 1,000 to 1 in 25,000. Some conditions have possible increased or decreased genetic risk of schizophrenia (22q11.2 deletion and duplication), or risk of aortic dilation (7q11.23 duplication) versus aortic stenosis (7q11.23 deletion). Many of these conditions are associated with developmental delay, autism, and/or multiple congenital anomalies and would not be detected with a karyotype. Chromosomal microarray analysis will detect all these conditions with a single screening test, allowing for the appropriate diagnosis and management of these patients. [Pediatr Ann. 2018;47(5):e198-e203.].
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20
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Varga NÁ, Pentelényi K, Balicza P, Gézsi A, Reményi V, Hársfalvi V, Bencsik R, Illés A, Prekop C, Molnár MJ. Mitochondrial dysfunction and autism: comprehensive genetic analyses of children with autism and mtDNA deletion. Behav Brain Funct 2018; 14:4. [PMID: 29458409 PMCID: PMC5819172 DOI: 10.1186/s12993-018-0135-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/16/2018] [Indexed: 12/27/2022] Open
Abstract
Background The etiology of autism spectrum disorders (ASD) is very heterogeneous. Mitochondrial dysfunction has been described in ASD; however, primary mitochondrial disease has been genetically proven in a small subset of patients. The main goal of the present study was to investigate correlations between mitochondrial DNA (mtDNA) changes and alterations of genes associated with mtDNA maintenance or ASD. Methods Sixty patients with ASD and sixty healthy individuals were screened for common mtDNA mutations. Next generation sequencing was performed on patients with major mtDNA deletions (mtdel-ASD) using two gene panels to investigate nuclear genes that are associated with ASD or are responsible for mtDNA maintenance. Cohorts of healthy controls, ASD patients without mtDNA alterations, and patients with mitochondrial disorders (non-ASD) harbouring mtDNA deletions served as comparison groups. Results MtDNA deletions were confirmed in 16.6% (10/60) of patients with ASD (mtdel-ASD). In 90% of this mtdel-ASD children we found rare SNVs in ASD-associated genes (one of those was pathogenic). In the intergenomic panel of this cohort one likely pathogenic variant was present. In patients with mitochondrial disease in genes responsible for mtDNA maintenance pathogenic mutations and variants of uncertain significance (VUS) were detected more frequently than those found in patients from the mtdel-ASD or other comparison groups. In healthy controls and in patients without a mtDNA deletion, only VUS were detected in both panel. Conclusions MtDNA alterations are more common in patients with ASD than in control individuals. MtDNA deletions are not isolated genetic alterations found in ASD; they coexist either with other ASD-associated genetic risk factors or with alterations in genes responsible for intergenomic communication. These findings indicate that mitochondrial dysfunction is not rare in ASD. The occurring mtDNA deletions in ASD may be mostly a consequence of the alterations of the causative culprit genes for autism or genes responsible for mtDNA maintenance, or because of the harmful effect of environmental factors. Electronic supplementary material The online version of this article (10.1186/s12993-018-0135-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Noémi Ágnes Varga
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary
| | - Klára Pentelényi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary
| | - Péter Balicza
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary
| | - András Gézsi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary.,Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary
| | - Viktória Reményi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary
| | - Vivien Hársfalvi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary
| | - Renáta Bencsik
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary
| | - Anett Illés
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary
| | - Csilla Prekop
- Vadaskert Foundation for Children's Mental Health, Lipótmezei Str. 1-5, Budapest, 1021, Hungary
| | - Mária Judit Molnár
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Tömő Str. 25-29, Budapest, 1083, Hungary.
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21
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Wang WB, Jia YC, Zhang Z, Xu J, Zuo RT, Kang QL. A novel duplication downstream of BMP2 in a Chinese family with Brachydactyly type A2 (BDA2). Gene 2018; 642:110-115. [DOI: 10.1016/j.gene.2017.11.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/16/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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23
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Praticò AD, Falsaperla R, Rizzo R, Ruggieri M, Verrotti A, Pavone P. A New Patient with Potocki-Lupski Syndrome: A Literature Review. J Pediatr Genet 2017; 7:29-34. [PMID: 29441219 DOI: 10.1055/s-0037-1604479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/29/2017] [Indexed: 12/14/2022]
Abstract
Speech delay, intellectual disability, and behavioral disturbances are the main clinical manifestations of Potocki-Lupski syndrome. Other features include infantile hypotonia, the absence of major dysmorphism, sleep disorders, and congenital anomalies, particularly of the cardiovascular system. A male patient with Potocki-Lupski syndrome is reported herein. He showed speech and borderline cognitive delay, behavioral troubles with no signs suggestive of autism, in the absence of major dysmorphism. A de novo 17p12-p11.2 duplication spanning 3.6 Mb was detected, with boundaries from 15,284,052 to 18,647,233 (hg19 assembly). At the age of 5 years, the child showed a noticeable improvement of speech skills and a moderate scholastic performance was reached. Upon analysis of the clinical manifestations of the present patient and those reported in existing literature, we found that the syndrome may present in various degrees of clinical expressivity. Affected patients may manifest symptoms ranging from mild behavioral disturbances to severe degrees of autism.
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Affiliation(s)
- Andrea Domenico Praticò
- Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.,Maurice Wohl Clinical Neuroscience Institute, King's College London, London, United Kingdom
| | - Raffaele Falsaperla
- Division of Pediatrics and Pediatric Emergency, University-Hospital "Policlinico-Vittorio Emanuele," University of Catania, Catania, Italy
| | - Renata Rizzo
- Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Martino Ruggieri
- Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | - Piero Pavone
- Division of Pediatrics and Pediatric Emergency, University-Hospital "Policlinico-Vittorio Emanuele," University of Catania, Catania, Italy
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24
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Garay PM, Wallner MA, Iwase S. Yin-yang actions of histone methylation regulatory complexes in the brain. Epigenomics 2016; 8:1689-1708. [PMID: 27855486 PMCID: PMC5289040 DOI: 10.2217/epi-2016-0090] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/05/2016] [Indexed: 02/07/2023] Open
Abstract
Dysregulation of histone methylation has emerged as a major driver of neurodevelopmental disorders including intellectual disabilities and autism spectrum disorders. Histone methyl writer and eraser enzymes generally act within multisubunit complexes rather than in isolation. However, it remains largely elusive how such complexes cooperate to achieve the precise spatiotemporal gene expression in the developing brain. Histone H3K4 methylation (H3K4me) is a chromatin signature associated with active gene-regulatory elements. We review a body of literature that supports a model in which the RAI1-containing H3K4me writer complex counterbalances the LSD1-containing H3K4me eraser complex to ensure normal brain development. This model predicts H3K4me as the nexus of previously unrelated neurodevelopmental disorders.
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Affiliation(s)
- Patricia Marie Garay
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Shigeki Iwase
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI 48109, USA
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25
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Zhu W, Mitsuhashi S, Yonekawa T, Noguchi S, Huei JCY, Nalini A, Preethish-Kumar V, Yamamoto M, Murakata K, Mori-Yoshimura M, Kamada S, Yahikozawa H, Karasawa M, Kimura S, Yamashita F, Nishino I. Missing genetic variations in GNE myopathy: rearrangement hotspots encompassing 5'UTR and founder allele. J Hum Genet 2016; 62:159-166. [PMID: 27829678 DOI: 10.1038/jhg.2016.134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/17/2016] [Accepted: 09/30/2016] [Indexed: 01/07/2023]
Abstract
GNE myopathy is an autosomal recessive distal myopathy caused by loss-of-function mutations in the GNE gene, which encodes UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE), a key enzyme in sialic-acid biosynthesis. By comprehensive screening of manifesting patients using a fine-mapped targeted next-generation sequencing (NGS), we identified copy number variations (CNVs) in 13 patients from 11 unrelated families. The nine unique CNVs largely vary in size from 0.3 to 72 kb. Over half of the cases carry different deletions spanning merely exon 2, which contains the 5' untranslated region (5'UTR) of the muscle major transcript hGNE1. Of most unique CNVs, either the telomeric or the centromeric breakpoint locates within intron 2, indicating rearrangement hotspots. Haplotype analysis suggested the existence of a founder allele with exon 2 deletion. The breakpoints for all CNVs were determined by long-range PCR and sequencing. All of the breakpoints of gross deletion/duplications reside within directly oriented pairs of Alu repeats. The results of this study firstly widen the spectra of mutations to CNVs encompassing 5'UTR, underscoring the pivotal role of the hGNE1 transcript. Alu-mediated non-recurrent CNVs may have been overlooked in a wide variety of recessive phenotypes, especially in those associated with genomic Alu-rich genes such as GNE.
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Affiliation(s)
- Wenhua Zhu
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Satomi Mitsuhashi
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takahiro Yonekawa
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan
| | | | | | - Veeramani Preethish-Kumar
- Department of Clinical Neurosciences, National Institute of Mental Health and Neurosciences, Bangalore, India
| | | | - Kenji Murakata
- Department of Neurology, Kansai Electric Power Hospital, Osaka, Japan
| | - Madoka Mori-Yoshimura
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Sachiko Kamada
- Department of Neurology, Akita University Graduate School of Medicine, Akita, Japan
| | | | | | - Seigo Kimura
- Department of Neurology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | | | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center (MGC), National Center of Neurology and Psychiatry, Tokyo, Japan
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26
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Huang WH, Guenthner CJ, Xu J, Nguyen T, Schwarz LA, Wilkinson AW, Gozani O, Chang HY, Shamloo M, Luo L. Molecular and Neural Functions of Rai1, the Causal Gene for Smith-Magenis Syndrome. Neuron 2016; 92:392-406. [PMID: 27693255 DOI: 10.1016/j.neuron.2016.09.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/13/2016] [Accepted: 09/09/2016] [Indexed: 12/24/2022]
Abstract
Haploinsufficiency of Retinoic Acid Induced 1 (RAI1) causes Smith-Magenis syndrome (SMS), which is associated with diverse neurodevelopmental and behavioral symptoms as well as obesity. RAI1 encodes a nuclear protein but little is known about its molecular function or the cell types responsible for SMS symptoms. Using genetically engineered mice, we found that Rai1 preferentially occupies DNA regions near active promoters and promotes the expression of a group of genes involved in circuit assembly and neuronal communication. Behavioral analyses demonstrated that pan-neural loss of Rai1 causes deficits in motor function, learning, and food intake. These SMS-like phenotypes are produced by loss of Rai1 function in distinct neuronal types: Rai1 loss in inhibitory neurons or subcortical glutamatergic neurons causes learning deficits, while Rai1 loss in Sim1+ or SF1+ cells causes obesity. By integrating molecular and organismal analyses, our study suggests potential therapeutic avenues for a complex neurodevelopmental disorder.
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Affiliation(s)
- Wei-Hsiang Huang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Casey J Guenthner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Tiffany Nguyen
- Stanford Behavioral and Functional Neuroscience Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Lindsay A Schwarz
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alex W Wilkinson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Mehrdad Shamloo
- Stanford Behavioral and Functional Neuroscience Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Neurosciences Program, Stanford University, Stanford, CA 94305, USA.
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27
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Guo X, Delio M, Haque N, Castellanos R, Hestand MS, Vermeesch JR, Morrow BE, Zheng D. Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis. Hum Mol Genet 2016; 25:3754-3767. [PMID: 27436579 DOI: 10.1093/hmg/ddw221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 11/13/2022] Open
Abstract
Velo-cardio-facial syndrome/DiGeorge syndrome/22q11.2 deletion syndrome (22q11.2DS) is caused by meiotic non-allelic homologous recombination events between flanking low copy repeats termed LCR22A and LCR22D, resulting in a 3 million base pair (Mb) deletion. Due to their complex structure, large size and high sequence identity, genetic variation within LCR22s among different individuals has not been well characterized. In this study, we sequenced 13 BAC clones derived from LCR22A/D and aligned them with 15 previously available BAC sequences to create a new genetic variation map. The thousands of variants identified by this analysis were not uniformly distributed in the two LCR22s. Moreover, shared single nucleotide variants between LCR22A and LCR22D were enriched in the Breakpoint Cluster Region pseudogene (BCRP) block, suggesting the existence of a possible recombination hotspot there. Interestingly, breakpoints for atypical 22q11.2 rearrangements have previously been located to BCRPs To further explore this finding, we carried out in-depth analyses of whole genome sequence (WGS) data from two unrelated probands harbouring a de novo 3Mb 22q11.2 deletion and their normal parents. By focusing primarily on WGS reads uniquely mapped to LCR22A, using the variation map from our BAC analysis to help resolve allele ambiguity, and by performing PCR analysis, we infer that the deletion breakpoints were most likely located near or within the BCRP module. In summary, we found a high degree of sequence variation in LCR22A and LCR22D and a potential recombination breakpoint near or within the BCRP block, providing a starting point for future breakpoint mapping using additional trios.
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Affiliation(s)
| | | | | | | | | | | | | | - Deyou Zheng
- Department of Neurology .,Department of Genetics.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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28
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Schumann M, Hofmann A, Krutzke SK, Hilger AC, Marsch F, Stienen D, Gembruch U, Ludwig M, Merz WM, Reutter H. Array-based molecular karyotyping in fetuses with isolated brain malformations identifies disease-causing CNVs. J Neurodev Disord 2016; 8:11. [PMID: 27087860 PMCID: PMC4832534 DOI: 10.1186/s11689-016-9144-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/15/2016] [Indexed: 11/21/2022] Open
Abstract
Background The overall birth prevalence for congenital malformations of the central nervous system (CNS) among Europeans may be as high as 1 in 100 live births. The etiological factors remain largely unknown. The aim of this study was to detect causative copy number variations (CNVs) in fetuses of terminated pregnancies with prenatally detected isolated brain malformations. Methods Array-based molecular karyotyping was performed in a cohort of 35 terminated fetuses with isolated CNS malformations. Identified putative disease-causing CNVs were confirmed using quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification. Results Based on their de novo occurrence and/or their established association with congenital brain malformations, we detected five disease-causing CNVs in four fetuses involving chromosomal regions 6p25.1-6p25.3 (FOXC1), 6q27, 16p12.3, Xp22.2-Xp22.32 (MID1), and Xp22.32-Xp22.33. Furthermore, we detected a probably disease-causing CNV involving chromosomal region 3p26.3 in one fetus, and in addition, we detected 12 CNVs in nine fetuses of unknown clinical significance. All CNVs except for two were absent in 1307 healthy in-house controls (frequency <0.0008). Each of the two CNVs present in in-house controls was present only once (frequency = 0.0008). Furthermore, our data suggests the involvement of CNTN6 and KLHL15 in the etiology of agenesis of the corpus callosum, the involvement of RASD1 and PTPRD in Dandy-Walker malformation, and the involvement of ERMARD in ventriculomegaly. Conclusions Our study suggests that CNVs play an important role in the etiology of isolated brain malformations.
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Affiliation(s)
- Madita Schumann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | | | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Florian Marsch
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Waltraut M Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Neonatology and Pediatric Intensive Care & Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
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29
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Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Hospital, Houston, Texas 77030, USA
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30
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Abstract
During meiosis, numerous DNA double-strand breaks (DSBs) are formed as part of the normal developmental program. This seemingly destructive behavior is necessary for successful meiosis, since repair of the DSBs through homologous recombination (HR) helps to produce physical links between the homologous chromosomes essential for correct chromosome segregation later in meiosis. However, DSB formation at such a massive scale also introduces opportunities to generate gross chromosomal rearrangements. In this review, we explore ways in which meiotic DSBs can result in such genomic alterations.
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31
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Chen L, Tao Y, Song F, Yuan X, Wang J, Saffen D. Evidence for genetic regulation of mRNA expression of the dosage-sensitive gene retinoic acid induced-1 (RAI1) in human brain. Sci Rep 2016; 6:19010. [PMID: 26743651 DOI: 10.1038/srep19010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/02/2015] [Indexed: 12/12/2022] Open
Abstract
RAI1 (retinoic acid induced-1) is a dosage-sensitive gene that causes Smith-Magenis syndrome (SMS) when mutated or deleted and Potocki-Lupski Syndrome (PTLS) when duplicated, with psychiatric features commonly observed in both syndromes. How common genetic variants regulate this gene, however, is unknown. In this study, we found that RAI1 mRNA expression in Chinese prefrontal and temporal cortex correlate with genotypes of common single nucleotide polymorphisms (SNPs) located in the RAI1 5′-upstream region. Using genotype imputation, “R2-Δ2” analysis, and data from the RegulomeDB database, we identified SNPs rs4925102 and rs9907986 as possible regulatory variants, accounting for approximately 30–40% of the variance in RAI1 mRNA expression in both brain regions. Specifically, rs4925102 and rs9907986 are predicted to disrupt the binding of retinoic acid RXR-RAR receptors and the transcription factor DEAF1 (Deformed epidermal autoregulatory factor-1), respectively. Consistent with these predictions, we observed binding of RXRα and RARα to the predicted RAI1 target in chromatin immunoprecipitation assays. Retinoic acid is crucial for early development of the central neural system, and DEAF1 is associated with intellectual disability. The observation that a significant portion of RAI1 mRNA expression is genetically controlled raises the possibility that common RAI1 5′-region regulatory variants contribute more generally to psychiatric disorders.
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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:
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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] [What about the content of this article? (0)] [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.
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Alaimo JT, Mullegama SV, Thomas MA, Elsea SH. Copy number loss upstream of RAI1 uncovers gene expression regulatory region that may impact Potocki-Lupski syndrome diagnosis. Mol Cytogenet 2015; 8:75. [PMID: 26442755 PMCID: PMC4594966 DOI: 10.1186/s13039-015-0179-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/23/2015] [Indexed: 02/07/2023] Open
Abstract
The identification of structural variants of uncertain clinical significance is increasing; however, studies delineating the functional consequence of these variants in the pathogenicity of phenotypic features are lacking. Understanding the consequence of structural variants such as copy number alterations and their role in gene expression changes is paramount in order to perform a comprehensive analysis of genetic effects on phenotypic variation and disease. RAI1 is a dosage-sensitive essential neurodevelopmental gene. Copy number loss of RAI1 results in Smith-Magenis syndrome while copy number gain results in Potocki-Lupski syndrome. Here, we present a case of a six year old female with a newly identified maternally inherited copy number loss that lies within the Smith-Magenis syndrome common deletion region, but RAI1 copy number is normal. Integration of the Encyclopedia of DNA Elements (ENCODE) data at the affected region suggests that the deletion disrupts several cis-acting regulatory elements upstream of RAI1, such as multiple repressor sites and an insulator region. Gene expression studies revealed that both the proband and the mother have significantly elevated RAI1 mRNA levels suggesting that the structural variant alters gene expression regulation. The proband and the mother both have some features of Potocki-Lupski syndrome, while the child appears to be more affected with autistic-like features. Overall, our work demonstrates that the integration of ENCODE data with structural variants of uncertain significance aids in delineating a functional consequence to a genomic aberration and subsequent diagnosis.
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Affiliation(s)
- Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
| | - Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
| | - Mary Ann Thomas
- Department of Medical Genetics, Alberta Children's Hospital, University of Calgary, Calgary, AB CA T2N 1N4 Canada
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Lupski JR. Structural variation mutagenesis of the human genome: Impact on disease and evolution. Environ Mol Mutagen 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Room 604B, Houston, Texas
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Wang M, Beck CR, English AC, Meng Q, Buhay C, Han Y, Doddapaneni HV, Yu F, Boerwinkle E, Lupski JR, Muzny DM, Gibbs RA. PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics 2015; 16:214. [PMID: 25887218 PMCID: PMC4376517 DOI: 10.1186/s12864-015-1370-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/20/2015] [Indexed: 11/24/2022] Open
Abstract
Background Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently, large-insert whole genome sequencing (WGS) technologies from Pacific Biosciences (PacBio) enable analysis of chromosomal structural variations (SVs), but the cost to achieve the required sequence coverage across the entire human genome is high. Results We developed a method (termed PacBio-LITS) that combines oligonucleotide-based DNA target-capture enrichment technologies with PacBio large-insert library preparation to facilitate SV studies at specific chromosomal regions. PacBio-LITS provides deep sequence coverage at the specified sites at substantially reduced cost compared with PacBio WGS. The efficacy of PacBio-LITS is illustrated by delineating the breakpoint junctions of low copy repeat (LCR)-associated complex structural rearrangements on chr17p11.2 in patients diagnosed with Potocki–Lupski syndrome (PTLS; MIM#610883). We successfully identified previously determined breakpoint junctions in three PTLS cases, and also were able to discover novel junctions in repetitive sequences, including LCR-mediated breakpoints. The new information has enabled us to propose mechanisms for formation of these structural variants. Conclusions The new method leverages the cost efficiency of targeted capture-sequencing as well as the mappability and scaffolding capabilities of long sequencing reads generated by the PacBio platform. It is therefore suitable for studying complex SVs, especially those involving LCRs, inversions, and the generation of chimeric Alu elements at the breakpoints. Other genomic research applications, such as haplotype phasing and small insertion and deletion validation could also benefit from this technology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1370-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Adam C English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Harsha V Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, 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
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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Sanchez-Jimeno C, Bustamante-Aragonés A, Infantes-Barbero F, Rodriguez De Alba M, Ramos C, Trujillo-Tiebas MJ, Lorda-Sánchez I. Two interstitial rearrangements (16q deletion and 17p duplication) in a child with MR/MCA. Clin Case Rep 2014; 2:303-9. [PMID: 25548634 PMCID: PMC4270714 DOI: 10.1002/ccr3.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 01/28/2023] Open
Abstract
KEY CLINICAL MEASSAGE Patients with rare deletions in 16q12 and a duplication of 17p, both interstitial and de novo. Only seven cases have been described with these deletions and none of them presented other chromosomal abnormalities. The proband showed a complex phenotype with features found in patients with dup17p11.2 syndrome, deletions in 16q12.
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Affiliation(s)
| | - Ana Bustamante-Aragonés
- Department of Genetics, Fundación Jimenez Díaz, Avda Reyes Católicos 2, Madrid, Spain ; Centro de Investigaciones Biomédicas en Red en Enfermedades Raras (CIBERER) Madrid, Spain
| | | | - Marta Rodriguez De Alba
- Department of Genetics, Fundación Jimenez Díaz, Avda Reyes Católicos 2, Madrid, Spain ; Centro de Investigaciones Biomédicas en Red en Enfermedades Raras (CIBERER) Madrid, Spain
| | - Carmen Ramos
- Department of Genetics, Fundación Jimenez Díaz, Avda Reyes Católicos 2, Madrid, Spain ; Centro de Investigaciones Biomédicas en Red en Enfermedades Raras (CIBERER) Madrid, Spain
| | - María Jose Trujillo-Tiebas
- Department of Genetics, Fundación Jimenez Díaz, Avda Reyes Católicos 2, Madrid, Spain ; Centro de Investigaciones Biomédicas en Red en Enfermedades Raras (CIBERER) Madrid, Spain
| | - Isabel Lorda-Sánchez
- Department of Genetics, Fundación Jimenez Díaz, Avda Reyes Católicos 2, Madrid, Spain ; Centro de Investigaciones Biomédicas en Red en Enfermedades Raras (CIBERER) Madrid, Spain
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Baskin B, Stavropoulos DJ, Rebeiro PA, Orr J, Li M, Steele L, Marshall CR, Lemire EG, Boycott KM, Gibson W, Ray PN. Complex genomic rearrangements in the dystrophin gene due to replication-based mechanisms. Mol Genet Genomic Med 2014; 2:539-47. [PMID: 25614876 PMCID: PMC4303224 DOI: 10.1002/mgg3.108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023] Open
Abstract
Genomic rearrangements such as intragenic deletions and duplications are the most prevalent type of mutations in the dystrophin gene resulting in Duchenne and Becker muscular dystrophy (D/BMD). These copy number variations (CNVs) are nonrecurrent and can result from either nonhomologous end joining (NHEJ) or microhomology-mediated replication-dependent recombination (MMRDR). We characterized five DMD patients with complex genomic rearrangements using a combination of MLPA/mRNA transcript analysis/custom array comparative hybridization arrays (CGH) and breakpoint sequence analysis to investigate the mechanisms for these rearrangements. Two patients had complex rearrangements that involved microhomologies at breakpoints. One patient had a noncontiguous insertion of 89.7 kb chromosome 4 into intron 43 of DMD involving three breakpoints with 2–5 bp microhomology at the junctions. A second patient had an inversion of exon 44 flanked by intronic deletions with two breakpoint junctions each showing 2 bp microhomology. The third patient was a female with an inherited deletion of exon 47 in DMD on the maternal allele and a de novo noncontiguous duplication of exons 45–49 in DMD and MID1 on the paternal allele. The other two patients harbored complex noncontiguous duplications within the dystrophin gene. We propose a replication-based mechanisms for all five complex DMD rearrangements. This study identifies additional underlying mechanisms in DMD, and provides insight into the molecular bases of these genomic rearrangements.
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Affiliation(s)
- Berivan Baskin
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University Uppsala, Sweden ; The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada ; Department of Laboratory Medicine and Pathology, University of Toronto Toronto, Ontario, Canada ; Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Paige A Rebeiro
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Jennifer Orr
- Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Martin Li
- Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Leslie Steele
- Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada ; Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Edmond G Lemire
- Division of Medical Genetics, Royal University Hospital & University of Saskatchewan Saskatoon, Saskatchewan, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario Ottawa, Ontario, Canada
| | - William Gibson
- Department of Medical Genetics, Child and Family Research Institute, The University of British Columbia Vancouver, British Columbia, Canada
| | - Peter N Ray
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada ; Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada ; Department of Molecular Genetics, The University of Toronto Toronto, Ontario, Canada
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Magoulas PL, Liu P, Gelowani V, Soler-Alfonso C, Kivuva EC, Lupski JR, Potocki L. Inherited dup(17)(p11.2p11.2): Expanding the phenotype of the Potocki-Lupski syndrome. Am J Med Genet A 2013; 164A:500-4. [DOI: 10.1002/ajmg.a.36287] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/12/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Pilar L. Magoulas
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
- Texas Children's Hospital; Houston Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Violet Gelowani
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Claudia Soler-Alfonso
- Division of Medical Genetics; Department of Pediatrics; University of Texas Health Science Center at Houston; Houston Texas
| | - Emma C. Kivuva
- Royal Devon and Exeter NHS Foundation Trust; Exeter United Kingdom
| | - James R. Lupski
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
- Department of Pediatrics; Baylor College of Medicine; Houston Texas
- Texas Children's Hospital; Houston Texas
| | - Lorraine Potocki
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
- Texas Children's Hospital; Houston Texas
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Cao L, Molina J, Abad C, Carmona-Mora P, Cárdenas Oyarzo A, Young JI, Walz K. Correct developmental expression level of Rai1 in forebrain neurons is required for control of body weight, activity levels and learning and memory. Hum Mol Genet 2013; 23:1771-82. [DOI: 10.1093/hmg/ddt568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Carvalho CM, Pehlivan D, Ramocki MB, Fang P, Alleva B, Franco LM, Belmont JW, Hastings PJ, Lupski JR. Replicative mechanisms for CNV formation are error prone. Nat Genet 2013; 45:1319-26. [PMID: 24056715 DOI: 10.1038/ng.2768] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 08/27/2013] [Indexed: 01/20/2023]
Abstract
We investigated 67 breakpoint junctions of gene copy number gains (CNVs) in 31 unrelated subjects. We observed a strikingly high frequency of small deletions and insertions (29%) apparently originating from polymerase-slippage events, in addition to frameshifts and point mutations in homonucleotide runs (13%), at or flanking the breakpoint junctions of complex CNVs. These simple nucleotide variants (SNV) were generated concomitantly with the de novo complex genomic rearrangement (CGR) event. Our findings implicate a low fidelity error-prone DNA polymerase in synthesis associated with DNA repair mechanisms that leads to a local increase in point mutation burden associated with human CGR.
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Lee CG, Park SJ, Yim SY, Sohn YB. Clinical and cytogenetic features of a Potocki-Lupski syndrome with the shortest 0.25Mb microduplication in 17p11.2 including RAI1. Brain Dev 2013; 35:681-5. [PMID: 23078968 DOI: 10.1016/j.braindev.2012.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
Abstract
Potocki-Lupski syndrome (PTLS [MIM 610883]) is a recently recognized microduplication syndrome associated with 17p11.2. It is characterized by mild facial dysmorphic features, hypermetropia, infantile hypotonia, failure to thrive, mental retardation, autistic spectrum disorders, behavioral abnormalities, sleep apnea, and cardiovascular anomalies. In several studies, the critical PTLS region was deduced to be 1.3Mb in length, and included RAI1 and 17 other genes. We report a 3-year-old Korean boy with the smallest duplication in 17p11.2 and a milder phenotype. He had no family history of neurologic disease or developmental delay and no history of seizure, autistic features, or behavior problems. He showed subtle facial dysmorphic features (dolichocephaly and a mildly asymmetric smile) and flat feet. All laboratory tests were normal and he had no evidence of internal organ anomalies. He was found to have mild intellectual disabilities (full scale IQ 65 on K-WPPSI) and language developmental delay (age of 2.2year-old on PRESS). Array comparative genomic hybridization (CGH) showed about a 0.25Mb microduplication on chromosome 17p11.2 containing four Refseq (NCBI reference sequence) genes, including RAI1 [arr 17p11.2(17,575,978-17,824,623)×3]. When compared with previously reported cases, the milder phenotype of our patient may be associated with the smallest duplication in 17p11.2, 0.25Mb in length.
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Affiliation(s)
- Cha Gon Lee
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, South Korea
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Ishmukhametova A, Chen JM, Bernard R, de Massy B, Baudat F, Boyer A, Méchin D, Thorel D, Chabrol B, Vincent MC, Khau Van Kien P, Claustres M, Tuffery-Giraud S. Dissecting the Structure and Mechanism of a Complex Duplication-Triplication Rearrangement in theDMDGene. Hum Mutat 2013; 34:1080-4. [DOI: 10.1002/humu.22353] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/27/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Aliya Ishmukhametova
- Université Montpellier 1; UFR médecine; Montpellier F-34000 France
- CHU Montpellier, Hôpital Arnaud de Villeneuve; Laboratoire de Génétique Moléculaire; Montpellier F-34000 France
| | - Jian-Min Chen
- INSERM U1078 and Établissement Français du Sang (EFS) - Bretagne; Brest F-29218 France
| | - Rafaëlle Bernard
- Laboratoire de Génétique Moléculaire; Hôpital de la Timone CHU; Marseille F-13385 France
| | - Bernard de Massy
- Institut de Génétique Humaine; UPR1142, CNRS; Montpellier France
| | - Frédéric Baudat
- Institut de Génétique Humaine; UPR1142, CNRS; Montpellier France
| | - Amandine Boyer
- Laboratoire de Génétique Moléculaire; Hôpital de la Timone CHU; Marseille F-13385 France
| | - Déborah Méchin
- CHU Montpellier, Hôpital Arnaud de Villeneuve; Laboratoire de Génétique Moléculaire; Montpellier F-34000 France
| | - Delphine Thorel
- CHU Montpellier, Hôpital Arnaud de Villeneuve; Laboratoire de Génétique Moléculaire; Montpellier F-34000 France
| | - Brigitte Chabrol
- CHU La Timone; Service de Neurologie Pédiatrique; Marseille F-13385 France
| | - Marie-Claire Vincent
- CHU Montpellier, Hôpital Arnaud de Villeneuve; Laboratoire de Génétique Moléculaire; Montpellier F-34000 France
| | - Philippe Khau Van Kien
- CHU Montpellier, Hôpital Arnaud de Villeneuve; Laboratoire de Génétique Moléculaire; Montpellier F-34000 France
| | - Mireille Claustres
- Université Montpellier 1; UFR médecine; Montpellier F-34000 France
- CHU Montpellier, Hôpital Arnaud de Villeneuve; Laboratoire de Génétique Moléculaire; Montpellier F-34000 France
- INSERM, U827; Montpellier F-34000 France
| | - Sylvie Tuffery-Giraud
- Université Montpellier 1; UFR médecine; Montpellier F-34000 France
- INSERM, U827; Montpellier F-34000 France
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Carter RD, Raia M, Ewing‐Cobbs L, Gambello M, Hashmi SS, Peterson SK, Robbins‐Furman P, Potocki L. Stress and Well‐Being Among Parents of Children with Potocki‐Lupski Syndrome. J Genet Couns 2013; 22:633-42. [DOI: 10.1007/s10897-013-9602-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 04/14/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Rebecca D. Carter
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of Texas Medical School at Houston6410 Fannin St., Ste. 1217HoustonTX77030USA
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of Texas Medical School at HoustonHoustonTXUSA
| | - Marianna Raia
- Department of Pediatrics Division of Medical GeneticsUniversity of Texas Medical School at HoustonHoustonTXUSA
| | - Linda Ewing‐Cobbs
- Children's Learning Institute Department of PediatricsUniversity of Texas Medical School at HoustonHoustonTXUSA
| | - Michael Gambello
- Department of Human GeneticsEmory University School of MedicineAtlantaGAUSA
| | - S. Shahrukh Hashmi
- Department of Pediatrics ‐ Pediatric Research CenterUniversity of Texas Medical School at HoustonHoustonTXUSA
| | - Susan K. Peterson
- Department of Behavioral ScienceThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Patricia Robbins‐Furman
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of Texas Medical School at Houston6410 Fannin St., Ste. 1217HoustonTX77030USA
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of Texas Medical School at HoustonHoustonTXUSA
| | - Lorraine Potocki
- Department of Molecular and Human GeneticsBaylor College of Medicine, Texas Children's HospitalHoustonTXUSA
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Bravo C, Gámez F, Pérez R, Águarón A, De León-Luis J. Prenatal diagnosis of Potocki-Lupski syndrome in a fetus with hypoplastic left heart and aberrant right subclavian artery. J Perinatol 2013; 33:394-6. [PMID: 23624966 DOI: 10.1038/jp.2012.77] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Potocki-Lupski syndrome (PTLS) is a rare genetic disorder associated with neurodevelopmental delay and heart defects. We report the first case of prenatal diagnosis of PTLS in a fetus with hypoplastic left heart and aberrant right subclavian artery. Detection of a fetal heart defect should be followed by chromosomal and genetic studies in order to rule out fetal aneuploidy and/or associated genetic syndromes with significant implications for the treatment of children with PTLS.
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Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res 2013; 23:762-76. [PMID: 23410887 PMCID: PMC3638133 DOI: 10.1101/gr.143677.112] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tumor genomes are generally thought to evolve through a gradual accumulation of mutations, but the observation that extraordinarily complex rearrangements can arise through single mutational events suggests that evolution may be accelerated by punctuated changes in genome architecture. To assess the prevalence and origins of complex genomic rearrangements (CGRs), we mapped 6179 somatic structural variation breakpoints in 64 cancer genomes from seven tumor types and screened for clusters of three or more interconnected breakpoints. We find that complex breakpoint clusters are extremely common: 154 clusters comprise 25% of all somatic breakpoints, and 75% of tumors exhibit at least one complex cluster. Based on copy number state profiling, 63% of breakpoint clusters are consistent with being CGRs that arose through a single mutational event. CGRs have diverse architectures including focal breakpoint clusters, large-scale rearrangements joining clusters from one or more chromosomes, and staggeringly complex chromothripsis events. Notably, chromothripsis has a significantly higher incidence in glioblastoma samples (39%) relative to other tumor types (9%). Chromothripsis breakpoints also show significantly elevated intra-tumor allele frequencies relative to simple SVs, which indicates that they arise early during tumorigenesis or confer selective advantage. Finally, assembly and analysis of 4002 somatic and 6982 germline breakpoint sequences reveal that somatic breakpoints show significantly less microhomology and fewer templated insertions than germline breakpoints, and this effect is stronger at CGRs than at simple variants. These results are inconsistent with replication-based models of CGR genesis and strongly argue that nonhomologous repair of concurrently arising DNA double-strand breaks is the predominant mechanism underlying complex cancer genome rearrangements.
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Affiliation(s)
- Ankit Malhotra
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22903, USA
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Abstract
Potocki-Lupski syndrome results from the duplication of chromosome 17 band p11.2. This is the first report of a case of Potocki-Lupski syndrome with teratologic dislocation of both hips. The diagnosis was made by chromosomal analysis. The association between Potocki-Lupski syndrome and musculoskeletal disorders may help elucidate the etiology and prognosis of the syndrome.
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Lee CG, Park SJ, Yun JN, Yim SY, Sohn YB. Reciprocal deletion and duplication of 17p11.2-11.2: Korean patients with Smith-Magenis syndrome and Potocki-Lupski syndrome. J Korean Med Sci 2012; 27:1586-90. [PMID: 23255863 PMCID: PMC3524443 DOI: 10.3346/jkms.2012.27.12.1586] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 08/14/2012] [Indexed: 11/24/2022] Open
Abstract
Deletion and duplication of the -3.7-Mb region in 17p11.2 result in two reciprocal syndrome, Smith-Magenis syndrome and Potocki-Lupski syndrome. Smith-Magenis syndrome is a well-known developmental disorder. Potocki-Lupski syndrome has recently been recognized as a microduplication syndrome that is a reciprocal disease of Smith-Magenis syndrome. In this paper, we report on the clinical and cytogenetic features of two Korean patients with Smith-Magenis syndrome and Potocki-Lupski syndrome. Patient 1 (Smith-Magenis syndrome) was a 2.9-yr-old boy who showed mild dysmorphic features, aggressive behavioral problems, and developmental delay. Patient 2 (Potocki-Lupski syndrome), a 17-yr-old boy, had only intellectual disabilities and language developmental delay. We used array comparative genomic hybridization (array CGH) and found a 2.6 Mb-sized deletion and a reciprocal 2.1 Mb-sized duplication involving the 17p11.2. These regions overlapped in a 2.1 Mb size containing 11 common genes, including RAI1 and SREBF.
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Affiliation(s)
- Cha Gon Lee
- Department of Pediatrics, Eulji General Hospital, Seoul, Korea
| | | | - Jun-No Yun
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Shin-Young Yim
- Department of Physical Medicine and Rehabilitation, Ajou University School of Medicine, Suwon, Korea
| | - Young Bae Sohn
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
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Popowski T, Molina-Gomes D, Loeuillet L, Boukobza P, Roume J, Vialard F. Prenatal diagnosis of the duplication 17p11.2 associated with Potocki–Lupski syndrome in a foetus presenting with mildly dysmorphic features. Eur J Med Genet 2012; 55:723-6. [DOI: 10.1016/j.ejmg.2012.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 08/17/2012] [Indexed: 11/17/2022]
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