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Cipolla C, Sessa L, Rotunno G, Sodero G, Proli F, Veredice C, Giorgio V, Leoni C, Rosati J, Limongelli D, Kuczynska E, Sforza E, Trevisan V, Rigante D, Zampino G, Onesimo R. Metabolic Profile of Patients with Smith-Magenis Syndrome: An Observational Study with Literature Review. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1451. [PMID: 37761412 PMCID: PMC10527612 DOI: 10.3390/children10091451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Background: Smith-Magenis syndrome (SMS) is caused by either interstitial deletions in the 17p11.2 region or pathogenic variants in the RAI1 gene and is marked by a distinct set of physical, developmental, neurological, and behavioral features. Hypercholesterolemia has been described in SMS, and obesity is also commonly found. Aim: To describe and characterize the metabolic phenotype of a cohort of SMS patients with an age range of 2.9-32.4 years and to evaluate any correlations between their body mass index and serum lipids, glycated hemoglobin (HbA1c), and basal insulin levels. Results: Seven/thirty-five patients had high values of both total cholesterol and low-density lipoprotein cholesterol; 3/35 had high values of triglycerides; none of the patients with RAI1 variants presented dyslipidemia. No patients had abnormal fasting glucose levels. Three/thirty-five patients had HbA1c in the prediabetes range. Ten/twenty-two patients with 17p11.2 deletion and 2/3 with RAI1 variants had increased insulin basal levels. Three/twenty-three patients with the 17p11.2 deletion had prediabetes. Conclusion: Our investigation suggests that SMS 'deleted' patients may show a dyslipidemic pattern, while SMS 'mutated' patients are more likely to develop early-onset obesity along with hyperinsulinism.
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Affiliation(s)
- Clelia Cipolla
- Pediatric Unit, Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy; (C.C.); (G.Z.); (R.O.)
| | - Linda Sessa
- Università Cattolica Sacro Cuore, 00168 Rome, RM, Italy
| | | | | | - Francesco Proli
- Pediatric Unit, Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy; (C.C.); (G.Z.); (R.O.)
| | - Chiara Veredice
- Pediatric Unit, Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy; (C.C.); (G.Z.); (R.O.)
- Pediatric Neurology Unit, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, RM, Italy
| | - Valentina Giorgio
- Pediatric Unit, Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy; (C.C.); (G.Z.); (R.O.)
- Università Cattolica Sacro Cuore, 00168 Rome, RM, Italy
| | - Chiara Leoni
- Center for Rare Diseases and Birth Defect, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy
| | - Jessica Rosati
- Unità di Riprogrammazione Cellulare, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, FG, Italy
| | | | - Eliza Kuczynska
- Center for Rare Diseases and Birth Defect, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy
| | - Elisabetta Sforza
- Università Cattolica Sacro Cuore, 00168 Rome, RM, Italy
- Center for Rare Diseases and Birth Defect, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy
| | - Valentina Trevisan
- Center for Rare Diseases and Birth Defect, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy
| | - Donato Rigante
- Pediatric Unit, Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy; (C.C.); (G.Z.); (R.O.)
- Università Cattolica Sacro Cuore, 00168 Rome, RM, Italy
- Center for Rare Diseases and Birth Defect, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy
| | - Giuseppe Zampino
- Pediatric Unit, Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy; (C.C.); (G.Z.); (R.O.)
- Università Cattolica Sacro Cuore, 00168 Rome, RM, Italy
- Center for Rare Diseases and Birth Defect, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy
| | - Roberta Onesimo
- Pediatric Unit, Department of Life Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy; (C.C.); (G.Z.); (R.O.)
- Center for Rare Diseases and Birth Defect, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, RM, Italy
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2
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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3
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Lupski JR. Biology in balance: human diploid genome integrity, gene dosage, and genomic medicine. Trends Genet 2022; 38:554-571. [PMID: 35450748 PMCID: PMC9222541 DOI: 10.1016/j.tig.2022.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
The path to completion of the functional annotation of the haploid human genome reference build, exploration of the clan genomics hypothesis, understanding human gene and genome functional biology, and gene genome and organismal evolution, is in reach.
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Affiliation(s)
- James R Lupski
- Genetics & Genomics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
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4
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Metabolic effects of the schizophrenia-associated 3q29 deletion. Transl Psychiatry 2022; 12:66. [PMID: 35177588 PMCID: PMC8854723 DOI: 10.1038/s41398-022-01824-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 01/14/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
The 1.6 Mb 3q29 deletion is associated with developmental and psychiatric phenotypes, including a 40-fold increased risk for schizophrenia. Reduced birth weight and a high prevalence of feeding disorders in patients suggest underlying metabolic dysregulation. We investigated 3q29 deletion-induced metabolic changes using our previously generated heterozygous B6.Del16+/Bdh1-Tfrc mouse model. Animals were provided either standard chow (STD) or high-fat diet (HFD). Growth curves were performed on HFD mice to assess weight change (n = 30-50/group). Indirect calorimetry and untargeted metabolomics were performed on STD and HFD mice to evaluate metabolic phenotypes (n = 8-14/group). A behavioral battery was performed on STD and HFD mice to assess behavior change after the HFD challenge (n = 5-13/group). We found that B6.Del16+/Bdh1-Tfrc animals preferentially use dietary lipids as an energy source. Untargeted metabolomics of liver tissue showed a strong sex-dependent effect of the 3q29 deletion on fat metabolism. A HFD partially rescued the 3q29 deletion-associated weight deficit in females, but not males. Untargeted metabolomics of liver tissue after HFD revealed persistent fat metabolism alterations in females. The HFD did not affect B6.Del16+/Bdh1-Tfrc behavioral phenotypes, suggesting that 3q29 deletion-associated metabolic and behavioral outcomes are uncoupled. Our data suggest that dietary interventions to improve weight phenotypes in 3q29 deletion syndrome patients are unlikely to exacerbate behavioral manifestations. Our study also highlights the importance of assessing sex in metabolic studies and suggests that mechanisms underlying 3q29 deletion-associated metabolic phenotypes are sex-specific.
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5
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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: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/26/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of heterogenous neurodevelopmental disorders affecting 1 in 59 children. Syndromic ASDs are commonly associated with chromosomal rearrangements or dosage imbalance involving a single gene. Many of these genes are dosage-sensitive and regulate transcription, protein homeostasis, and synaptic function in the brain. Despite vastly different molecular perturbations, syndromic ASDs share core symptoms including social dysfunction and repetitive behavior. However, each ASD subtype has a unique pathogenic mechanism and combination of comorbidities that require individual attention. We have learned a great deal about how these dosage-sensitive genes control brain development and behaviors from genetically-engineered mice. Here we describe the clinical features of eight monogenic neurodevelopmental disorders caused by dosage imbalance of four genes, as well as recent advances in using genetic mouse models to understand their pathogenic mechanisms and develop intervention strategies. We propose that applying newly developed quantitative molecular and neuroscience technologies will advance our understanding of the unique neurobiology of each disorder and enable the development of personalized therapy.
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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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6
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Venkatapoorna CMK, Ayine P, Parra EP, Koenigs T, Phillips M, Babu JR, Sandey M, Geetha T. Association of Salivary Amylase ( AMY1) Gene Copy Number with Obesity in Alabama Elementary School Children. Nutrients 2019; 11:nu11061379. [PMID: 31248128 PMCID: PMC6627241 DOI: 10.3390/nu11061379] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 01/14/2023] Open
Abstract
Salivary amylase (AMY1) is the most abundant enzyme in human saliva, responsible for the hydrolysis of α-1,4 glycosidic linkages that aids in the digestion of starch. Recently studies have shown that the copy number of AMY1 is associated with obesity; however, the data varies with location. One-third of children are overweight/obese in Alabama. In this study, we aim to determine the relationship between the copy number of AMY1 gene and obesity measurements in children from Alabama. One hundred twenty-seven children aged between 6 to 10 years participated in this study. Anthropometric measurements were measured using WHO recommendations. Genomic DNA was extracted from saliva, and the copy number of the AMY1 gene was estimated by digital PCR. The association between AMY1 copy number and obesity measurements was analyzed by linear regression. The mean AMY1 copy number significantly decreased in overweight/obese (6.21 ± 1.48) compared to normal weight (7.97 ± 2.35) children. AMY1 copy number inversely associated with the obesity measurements. African Americans had a stronger association between low AMY1 copy number and obesity compared to white/European Americans. Our findings suggest that overweight/obese children have a low AMY1 copy number and the effect is more prominent in African Americans.
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Affiliation(s)
- Chandra M K Venkatapoorna
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Priscilla Ayine
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Emily P Parra
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Taylor Koenigs
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Megan Phillips
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
| | - Jeganathan R Babu
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA.
| | - Maninder Sandey
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
| | - Thangiah Geetha
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA.
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA.
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7
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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] [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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8
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Takumi T, Tamada K, Hatanaka F, Nakai N, Bolton PF. Behavioral neuroscience of autism. Neurosci Biobehav Rev 2019; 110:60-76. [PMID: 31059731 DOI: 10.1016/j.neubiorev.2019.04.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 04/03/2019] [Accepted: 04/22/2019] [Indexed: 12/29/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Several genetic causes of ASD have been identified and this has enabled researchers to construct mouse models. Mouse behavioral tests reveal impaired social interaction and communication, as well as increased repetitive behavior and behavioral inflexibility in these mice, which correspond to core behavioral deficits observed in individuals with ASD. However, the connection between these behavioral abnormalities and the underlying dysregulation in neuronal circuits and synaptic function is poorly understood. Moreover, different components of the ASD phenotype may be linked to dysfunction in different brain regions, making it even more challenging to chart the pathophysiological mechanisms involved in ASD. Here we summarize the research on mouse models of ASD and their contribution to understanding pathophysiological mechanisms. Specifically, we emphasize abnormal serotonin production and regulation, as well as the disruption in circadian rhythms and sleep that are observed in a subset of ASD, and propose that spatiotemporal disturbances in brainstem development may be a primary cause of ASD that propagates towards the cerebral cortex.
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Affiliation(s)
- Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan.
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | | | - Nobuhiro Nakai
- RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan
| | - Patrick F Bolton
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK
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9
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Silva AI, Ulfarsson MO, Stefansson H, Gustafsson O, Walters GB, Linden DE, Wilkinson LS, Drakesmith M, Owen MJ, Hall J, Stefansson K. Reciprocal White Matter Changes Associated With Copy Number Variation at 15q11.2 BP1-BP2: A Diffusion Tensor Imaging Study. Biol Psychiatry 2019; 85:563-572. [PMID: 30583851 PMCID: PMC6424871 DOI: 10.1016/j.biopsych.2018.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND The 15q11.2 BP1-BP2 cytogenetic region has been associated with learning and motor delays, autism, and schizophrenia. This region includes a gene that codes for the cytoplasmic FMR1 interacting protein 1 (CYFIP1). The CYFIP1 protein is involved in actin cytoskeletal dynamics and interacts with the fragile X mental retardation protein. Absence of fragile X mental retardation protein causes fragile X syndrome. Because abnormal white matter microstructure has been reported in both fragile X syndrome and psychiatric disorders, we looked at the impact of 15q11.2 BP1-BP2 dosage on white matter microstructure. METHODS Combining a brain-wide voxel-based approach and a regional-based analysis, we analyzed diffusion tensor imaging data from healthy individuals with the deletion (n = 30), healthy individuals with the reciprocal duplication (n = 27), and IQ-matched control subjects with no large copy number variants (n = 19), recruited from a large genotyped population sample. RESULTS We found global mirror effects (deletion > control > duplication) on fractional anisotropy. The deletion group showed widespread increased fractional anisotropy when compared with duplication. Regional analyses revealed a greater effect size in the posterior limb of the internal capsule and a tendency for decreased fractional anisotropy in duplication. CONCLUSIONS These results show a reciprocal effect of 15q11.2 BP1-BP2 on white matter microstructure, suggesting that reciprocal chromosomal imbalances may lead to opposite changes in brain structure. Findings in the deletion overlap with previous white matter differences reported in fragile X syndrome patients, suggesting common pathogenic mechanisms derived from disruptions of cytoplasmic CYFIP1-fragile X mental retardation protein complexes. Our data begin to identify specific components of the 15q11.2 BP1-BP2 phenotype and neurobiological mechanisms of potential relevance to the increased risk for disorder.
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Affiliation(s)
- Ana I. Silva
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff, United Kingdom,Neuroscience and Mental Health Research Institute, Cardiff, United Kingdom,Division of Psychological Medicine and Clinical Neurosciences, Cardiff, United Kingdom
| | - Magnus O. Ulfarsson
- deCODE genetics/Amgen, Reykjavik, Iceland,Faculty of Electrical Engineering, Reykjavik, Iceland
| | | | | | - G. Bragi Walters
- deCODE genetics/Amgen, Reykjavik, Iceland,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - David E.J. Linden
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff, United Kingdom,Neuroscience and Mental Health Research Institute, Cardiff, United Kingdom,Division of Psychological Medicine and Clinical Neurosciences, Cardiff, United Kingdom
| | - Lawrence S. Wilkinson
- Neuroscience and Mental Health Research Institute, Cardiff, United Kingdom,Division of Psychological Medicine and Clinical Neurosciences, Cardiff, United Kingdom,MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Mark Drakesmith
- Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff, United Kingdom
| | - Michael J. Owen
- Neuroscience and Mental Health Research Institute, Cardiff, United Kingdom,Division of Psychological Medicine and Clinical Neurosciences, Cardiff, United Kingdom,MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Cardiff, United Kingdom; Division of Psychological Medicine and Clinical Neurosciences, Cardiff, United Kingdom; MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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10
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Lupski JR. 2018 Victor A. McKusick Leadership Award: Molecular Mechanisms for Genomic and Chromosomal Rearrangements. Am J Hum Genet 2019; 104:391-406. [PMID: 30849326 PMCID: PMC6407437 DOI: 10.1016/j.ajhg.2018.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA.
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11
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Chung RH, Chiu YF, Hung YJ, Lee WJ, Wu KD, Chen HL, Lin MW, Chen YDI, Quertermous T, Hsiung CA. Genome-wide copy number variation analysis identified deletions in SFMBT1 associated with fasting plasma glucose in a Han Chinese population. BMC Genomics 2017; 18:591. [PMID: 28789618 PMCID: PMC5549306 DOI: 10.1186/s12864-017-3975-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/31/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Fasting glucose and fasting insulin are glycemic traits closely related to diabetes, and understanding the role of genetic factors in these traits can help reveal the etiology of type 2 diabetes. Although single nucleotide polymorphisms (SNPs) in several candidate genes have been found to be associated with fasting glucose and fasting insulin, copy number variations (CNVs), which have been reported to be associated with several complex traits, have not been reported for association with these two traits. We aimed to identify CNVs associated with fasting glucose and fasting insulin. RESULTS We conducted a genome-wide CNV association analysis for fasting plasma glucose (FPG) and fasting plasma insulin (FPI) using a family-based genome-wide association study sample from a Han Chinese population in Taiwan. A family-based CNV association test was developed in this study to identify common CNVs (i.e., CNVs with frequencies ≥ 5%), and a generalized estimating equation approach was used to test the associations between the traits and counts of global rare CNVs (i.e., CNVs with frequencies <5%). We found a significant genome-wide association for common deletions with a frequency of 5.2% in the Scm-like with four mbt domains 1 (SFMBT1) gene with FPG (association p-value = 2×10-4 and an adjusted p-value = 0.0478 for multiple testing). No significant association was observed between global rare CNVs and FPG or FPI. The deletions in 20 individuals with DNA samples available were successfully validated using PCR-based amplification. The association of the deletions in SFMBT1 with FPG was further evaluated using an independent population-based replication sample obtained from the Taiwan Biobank. An association p-value of 0.065, which was close to the significance level of 0.05, for FPG was obtained by testing 9 individuals with CNVs in the SFMBT1 gene region and 11,692 individuals with normal copies in the replication cohort. CONCLUSIONS Previous studies have found that SNPs in SFMBT1 are associated with blood pressure and serum urate concentration, suggesting that SFMBT1 may have functional implications in some metabolic-related traits.
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Affiliation(s)
- Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan
| | - Yen-Feng Chiu
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Social Work, Tunghai University, Taichung, Taiwan
| | - Kwan-Dun Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Ling Chen
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan
| | - Ming-Wei Lin
- Institute of Public Health, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Yii-Der I Chen
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Stanford Cardiovascular Institute, Falk Cardiovascular Research Center, Stanford University, Stanford, California, USA
| | - Chao A Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, No 35, Keyan Road, Zhunan, Miaoli, 350, Taiwan.
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Recent progress in genetics, epigenetics and metagenomics unveils the pathophysiology of human obesity. Clin Sci (Lond) 2017; 130:943-86. [PMID: 27154742 DOI: 10.1042/cs20160136] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
In high-, middle- and low-income countries, the rising prevalence of obesity is the underlying cause of numerous health complications and increased mortality. Being a complex and heritable disorder, obesity results from the interplay between genetic susceptibility, epigenetics, metagenomics and the environment. Attempts at understanding the genetic basis of obesity have identified numerous genes associated with syndromic monogenic, non-syndromic monogenic, oligogenic and polygenic obesity. The genetics of leanness are also considered relevant as it mirrors some of obesity's aetiologies. In this report, we summarize ten genetically elucidated obesity syndromes, some of which are involved in ciliary functioning. We comprehensively review 11 monogenic obesity genes identified to date and their role in energy maintenance as part of the leptin-melanocortin pathway. With the emergence of genome-wide association studies over the last decade, 227 genetic variants involved in different biological pathways (central nervous system, food sensing and digestion, adipocyte differentiation, insulin signalling, lipid metabolism, muscle and liver biology, gut microbiota) have been associated with polygenic obesity. Advances in obligatory and facilitated epigenetic variation, and gene-environment interaction studies have partly accounted for the missing heritability of obesity and provided additional insight into its aetiology. The role of gut microbiota in obesity pathophysiology, as well as the 12 genes associated with lipodystrophies is discussed. Furthermore, in an attempt to improve future studies and merge the gap between research and clinical practice, we provide suggestions on how high-throughput '-omic' data can be integrated in order to get closer to the new age of personalized medicine.
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Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2432957. [PMID: 28428959 PMCID: PMC5385910 DOI: 10.1155/2017/2432957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/26/2017] [Accepted: 02/06/2017] [Indexed: 01/11/2023]
Abstract
Introduction. Increase in body weight is a gradual process that usually begins in childhood and in adolescence as a result of multiple interactions among environmental and genetic factors. This study aimed to analyze the relationship between copy number variants (CNVs) in five genes and four intergenic regions with obesity in Mexican children. Methods. We studied 1423 children aged 6–12 years. Anthropometric measurements and blood levels of biochemical parameters were obtained. Identification of CNVs was performed by real-time PCR. The effect of CNVs on obesity or body composition was assessed using regression models adjusted for age, gender, and family history of obesity. Results. Gains in copy numbers of LEPR and NEGR1 were associated with decreased body mass index (BMI), waist circumference (WC), and risk of abdominal obesity, whereas gain in ARHGEF4 and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d and losses in INS were associated with increased BMI and WC. Conclusion. Our results indicate a possible contribution of CNVs in LEPR, NEGR1, ARHGEF4, and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d to the development of obesity, particularly abdominal obesity in Mexican children.
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Knebel B, Lehr S, Janssen OE, Hahn S, Jacob S, Nitzgen U, Müller-Wieland D, Kotzka J. Association between copy-number variation on metabolic phenotypes and HDL-C levels in patients with polycystic ovary syndrome. Mol Biol Rep 2016; 44:51-61. [DOI: 10.1007/s11033-016-4080-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/09/2016] [Indexed: 01/08/2023]
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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: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [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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16
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Yuan B, Neira J, Gu S, Harel T, Liu P, Briceño I, Elsea SH, Gómez A, Potocki L, Lupski JR. Nonrecurrent PMP22-RAI1 contiguous gene deletions arise from replication-based mechanisms and result in Smith-Magenis syndrome with evident peripheral neuropathy. Hum Genet 2016; 135:1161-74. [PMID: 27386852 DOI: 10.1007/s00439-016-1703-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/21/2016] [Indexed: 11/29/2022]
Abstract
Hereditary neuropathy with liability to pressure palsies (HNPP) and Smith-Magenis syndrome (SMS) are genomic disorders associated with deletion copy number variants involving chromosome 17p12 and 17p11.2, respectively. Nonallelic homologous recombination (NAHR)-mediated recurrent deletions are responsible for the majority of HNPP and SMS cases; the rearrangement products encompass the key dosage-sensitive genes PMP22 and RAI1, respectively, and result in haploinsufficiency for these genes. Less frequently, nonrecurrent genomic rearrangements occur at this locus. Contiguous gene duplications encompassing both PMP22 and RAI1, i.e., PMP22-RAI1 duplications, have been investigated, and replication-based mechanisms rather than NAHR have been proposed for these rearrangements. In the current study, we report molecular and clinical characterizations of six subjects with the reciprocal phenomenon of deletions spanning both genes, i.e., PMP22-RAI1 deletions. Molecular studies utilizing high-resolution array comparative genomic hybridization and breakpoint junction sequencing identified mutational signatures that were suggestive of replication-based mechanisms. Systematic clinical studies revealed features consistent with SMS, including features of intellectual disability, speech and gross motor delays, behavioral problems and ocular abnormalities. Five out of six subjects presented clinical signs and/or objective electrophysiologic studies of peripheral neuropathy. Clinical profiling may improve the clinical management of this unique group of subjects, as the peripheral neuropathy can be more severe or of earlier onset as compared to SMS patients having the common recurrent deletion. Moreover, the current study, in combination with the previous report of PMP22-RAI1 duplications, contributes to the understanding of rare complex phenotypes involving multiple dosage-sensitive genes from a genetic mechanistic standpoint.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juanita Neira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ignacio Briceño
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
- Instituto de Referencia Andino, Bogotá, Colombia
- Facultad de Medicina, Universidad de La Sabana, Chía, Colombia
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alberto Gómez
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
- Instituto de Referencia Andino, Bogotá, Colombia
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Texas Children's Hospital, Houston, TX, 77030, USA.
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17
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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] [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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18
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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] [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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19
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Zhang F, Lupski JR. Non-coding genetic variants in human disease. Hum Mol Genet 2015; 24:R102-10. [PMID: 26152199 DOI: 10.1093/hmg/ddv259] [Citation(s) in RCA: 383] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/03/2015] [Indexed: 01/16/2023] Open
Abstract
Genetic variants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), in the non-coding regions of the human genome can play an important role in human traits and complex diseases. Most of the genome-wide association study (GWAS) signals map to non-coding regions and potentially point to non-coding variants, whereas their functional interpretation is challenging. In this review, we discuss the human non-coding variants and their contributions to human diseases in the following four parts. (i) Functional annotations of non-coding SNPs mapped by GWAS: we discuss recent progress revealing some of the molecular mechanisms for GWAS signals affecting gene function. (ii) Technical progress in interpretation of non-coding variants: we briefly describe some of the technologies for functional annotations of non-coding variants, including the methods for genome-wide mapping of chromatin interaction, computational tools for functional predictions and the new genome editing technologies useful for dissecting potential functional consequences of non-coding variants. (iii) Non-coding CNVs in human diseases: we review our emerging understanding the role of non-coding CNVs in human disease. (iv) Compound inheritance of large genomic deletions and non-coding variants: compound inheritance at a locus consisting of coding variants plus non-coding ones is described.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA and Texas Children's Hospital, Houston, TX 77030, USA
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20
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Lupski JR. Structural variation mutagenesis of the human genome: Impact on disease and evolution. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:419-36. [PMID: 25892534 PMCID: PMC4609214 DOI: 10.1002/em.21943] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 05/19/2023]
Abstract
Watson-Crick base-pair changes, or single-nucleotide variants (SNV), have long been known as a source of mutations. However, the extent to which DNA structural variation, including duplication and deletion copy number variants (CNV) and copy number neutral inversions and translocations, contribute to human genome variation and disease has been appreciated only recently. Moreover, the potential complexity of structural variants (SV) was not envisioned; thus, the frequency of complex genomic rearrangements and how such events form remained a mystery. The concept of genomic disorders, diseases due to genomic rearrangements and not sequence-based changes for which genomic architecture incite genomic instability, delineated a new category of conditions distinct from chromosomal syndromes and single-gene Mendelian diseases. Nevertheless, it is the mechanistic understanding of CNV/SV formation that has promoted further understanding of human biology and disease and provided insights into human genome and gene evolution. Environ. Mol. Mutagen. 56:419-436, 2015. © 2015 Wiley Periodicals, Inc.
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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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21
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Veerappa AM, Vishweswaraiah S, Lingaiah K, Murthy M, Suresh RV, Manjegowda DS, Ramachandra NB. Global spectrum of copy number variations reveals genome organizational plasticity and proposes new migration routes. PLoS One 2015; 10:e0121846. [PMID: 25909454 PMCID: PMC4409114 DOI: 10.1371/journal.pone.0121846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/16/2015] [Indexed: 11/19/2022] Open
Abstract
Global spectrum of CNVs is required to catalog variations to provide a high-resolution on the dynamics of genome-organization and human migration. In this study, we performed genome-wide genotyping using high-resolution arrays and identified 44,109 CNVs from 1,715 genomes across 12 populations. The study unraveled the force of independent evolutionary dynamics on genome-organizational plasticity across populations. We demonstrated the use of CNV tool to study human migration and identified a second major settlement establishing new migration routes in addition to existing ones.
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Affiliation(s)
- Avinash M. Veerappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Sangeetha Vishweswaraiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Kusuma Lingaiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Megha Murthy
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Raviraj V. Suresh
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
| | - Dinesh S. Manjegowda
- NUCSER, KS Hegde Medical Academy, Nitte University, Mangalore-18, Karnataka, India
| | - Nallur B. Ramachandra
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore-06, Karnataka, India
- * E-mail:
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22
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Lumaban JG, Nelson DL. The Fragile X proteins Fmrp and Fxr2p cooperate to regulate glucose metabolism in mice. Hum Mol Genet 2014; 24:2175-84. [PMID: 25552647 DOI: 10.1093/hmg/ddu737] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Fragile X syndrome results from loss of FMR1 expression. Individuals with the disorder exhibit not only intellectual disability, but also an array of physical and behavioral abnormalities, including sleep difficulties. Studies in mice demonstrated that Fmr1, along with its paralog Fxr2, regulate circadian behavior, and that their absence disrupts expression and cycling of essential clock mRNAs in the liver. Recent reports have identified circadian genes to be essential for normal metabolism. Here we describe the metabolic defects that arise in mice mutated for both Fmr1 and Fxr2. These mice have reduced fat deposits compared with age- and weight-matched controls. Several metabolic markers show either low levels in plasma or abnormal circadian cycling (or both). Insulin levels are consistently low regardless of light exposure and feeding conditions, and the animals are extremely sensitive to injected insulin. Glucose production from introduced pyruvate and glucagon is impaired and the mice quickly clear injected glucose. These mice also have higher food intake and higher VO2 and VCO2 levels. We analyzed liver expression of genes involved in glucose homeostasis and found several that are expressed differentially in the mutant mice. These results point to the involvement of Fmr1 and Fxr2 in maintaining the normal metabolic state in mice.
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Affiliation(s)
- Jeannette G Lumaban
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, 1250 Moursund Street, Houston, TX 77030, USA
| | - David L Nelson
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, 1250 Moursund Street, Houston, TX 77030, USA
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23
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Jackson FLC. Gene-environment interactions in human health: case studies and strategies for developing new paradigms and research methodologies. Front Genet 2014; 5:271. [PMID: 25221564 PMCID: PMC4148636 DOI: 10.3389/fgene.2014.00271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/23/2014] [Indexed: 01/25/2023] Open
Abstract
THE SYNERGISTIC EFFECTS OF GENES AND THE ENVIRONMENT ON HEALTH ARE EXPLORED IN THREE CASE STUDIES: adult lactase persistence, autism spectrum disorders, and the metabolic syndrome, providing examples of the interactive complexities underlying these phenotypes. Since the phenotypes are the initial targets of evolutionary processes, understanding the specific environmental contexts of the genetic, epigenetic, and environmental changes associated with these phenotypes is essential in predicting their health implications. Robust databases must be developed on the local scale to deconstruct both the population substructure and the unique components of the environment that stimulate geographically specific changes in gene expression patterns. To produce these databases and make valid predictions, new, locally focused, and information-dense models are needed that incorporate data on evolutionary ecology, environmental complexity, local geographic patterns of gene expression, and population substructure.
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Affiliation(s)
- Fatimah L C Jackson
- Department of Biology and W. Montague Cobb Research Laboratory, Howard University Washington, DC, USA
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24
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Alaimo JT, Hahn NH, Mullegama SV, Elsea SH. Dietary regimens modify early onset of obesity in mice haploinsufficient for Rai1. PLoS One 2014; 9:e105077. [PMID: 25127133 PMCID: PMC4134272 DOI: 10.1371/journal.pone.0105077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/18/2014] [Indexed: 01/10/2023] Open
Abstract
Smith-Magenis syndrome is a complex genomic disorder in which a majority of individuals are obese by adolescence. While an interstitial deletion of chromosome 17p11.2 is the leading cause, mutation or deletion of the RAI1 gene alone results in most features of the disorder. Previous studies have shown that heterozygous knockout of Rai1 results in an obese phenotype in mice and that Smith-Magenis syndrome mouse models have a significantly reduced fecundity and an altered transmission pattern of the mutant Rai1 allele, complicating large, extended studies in these models. In this study, we show that breeding C57Bl/6J Rai1+/− mice with FVB/NJ to create F1 Rai1+/− offspring in a mixed genetic background ameliorates both fecundity and Rai1 allele transmission phenotypes. These findings suggest that the mixed background provides a more robust platform for breeding and larger phenotypic studies. We also characterized the effect of dietary intake on Rai1+/− mouse growth during adolescent and early adulthood developmental stages. Animals fed a high carbohydrate or a high fat diet gained weight at a significantly faster rate than their wild type littermates. Both high fat and high carbohydrate fed Rai1+/− mice also had an increase in body fat and altered fat distribution patterns. Interestingly, Rai1+/− mice fed different diets did not display altered fasting blood glucose levels. These results suggest that dietary regimens are extremely important for individuals with Smith- Magenis syndrome and that food high in fat and carbohydrates may exacerbate obesity outcomes.
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Affiliation(s)
- Joseph T. Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Natalie H. Hahn
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Sureni V. Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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25
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Veerappa AM, N MM, Vishweswaraiah S, Lingaiah K, Suresh RV, Nachappa SA, Prashali N, Yadav SN, Srikanta MA, Manjegowda DS, Seshachalam KB, Ramachandra NB. Copy number variations burden on miRNA genes reveals layers of complexities involved in the regulation of pathways and phenotypic expression. PLoS One 2014; 9:e90391. [PMID: 24587348 PMCID: PMC3938728 DOI: 10.1371/journal.pone.0090391] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (∼ 9%) consisting 6542 (∼ 5%) miRNA genes with a total of 333 (∼ 5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity.
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Affiliation(s)
- Avinash M. Veerappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Megha Murthy N
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Sangeetha Vishweswaraiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Kusuma Lingaiah
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Raviraj V. Suresh
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Somanna Ajjamada Nachappa
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Nelchi Prashali
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Sangeetha Nuggehalli Yadav
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Manjula Arsikere Srikanta
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Dinesh S. Manjegowda
- Department of Anatomy, Yenepoya Medical College, Yenepoya University, Mangalore, Karnataka, India
- Nitte University Centre for Science Education & Research, K S Hegde Medical Academy, Nitte University, Deralakatte, Mangalore, Karnataka, India
| | | | - Nallur B. Ramachandra
- Genetics and Genomics Lab, Department of Studies in Zoology, University of Mysore, Manasagangotri, Mysore, Karnataka, India
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26
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Dauber A, Golzio C, Guenot C, Jodelka FM, Kibaek M, Kjaergaard S, Leheup B, Martinet D, Nowaczyk MJM, Rosenfeld JA, Zeesman S, Zunich J, Beckmann JS, Hirschhorn JN, Hastings ML, Jacquemont S, Katsanis N. SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the 8q24.3 copy-number variant. Am J Hum Genet 2013; 93:798-811. [PMID: 24140112 DOI: 10.1016/j.ajhg.2013.09.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/10/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
Copy-number variants (CNVs) represent a significant interpretative challenge, given that each CNV typically affects the dosage of multiple genes. Here we report on five individuals with coloboma, microcephaly, developmental delay, short stature, and craniofacial, cardiac, and renal defects who harbor overlapping microdeletions on 8q24.3. Fine mapping localized a commonly deleted 78 kb region that contains three genes: SCRIB, NRBP2, and PUF60. In vivo dissection of the CNV showed discrete contributions of the planar cell polarity effector SCRIB and the splicing factor PUF60 to the syndromic phenotype, and the combinatorial suppression of both genes exacerbated some, but not all, phenotypic components. Consistent with these findings, we identified an individual with microcephaly, short stature, intellectual disability, and heart defects with a de novo c.505C>T variant leading to a p.His169Tyr change in PUF60. Functional testing of this allele in vivo and in vitro showed that the mutation perturbs the relative dosage of two PUF60 isoforms and, subsequently, the splicing efficiency of downstream PUF60 targets. These data inform the functions of two genes not associated previously with human genetic disease and demonstrate how CNVs can exhibit complex genetic architecture, with the phenotype being the amalgam of both discrete dosage dysfunction of single transcripts and also of binary genetic interactions.
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Affiliation(s)
- Andrew Dauber
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02115, USA
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27
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Goldlust IS, Hermetz KE, Catalano LM, Barfield RT, Cozad R, Wynn G, Ozdemir AC, Conneely KN, Mulle JG, Dharamrup S, Hegde MR, Kim KH, Angle B, Colley A, Webb AE, Thorland EC, Ellison JW, Rosenfeld JA, Ballif BC, Shaffer LG, Demmer LA, Rudd MK. Mouse model implicates GNB3 duplication in a childhood obesity syndrome. Proc Natl Acad Sci U S A 2013; 110:14990-4. [PMID: 23980137 PMCID: PMC3773733 DOI: 10.1073/pnas.1305999110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Obesity is a highly heritable condition and a risk factor for other diseases, including type 2 diabetes, cardiovascular disease, hypertension, and cancer. Recently, genomic copy number variation (CNV) has been implicated in cases of early onset obesity that may be comorbid with intellectual disability. Here, we describe a recurrent CNV that causes a syndrome associated with intellectual disability, seizures, macrocephaly, and obesity. This unbalanced chromosome translocation leads to duplication of over 100 genes on chromosome 12, including the obesity candidate gene G protein β3 (GNB3). We generated a transgenic mouse model that carries an extra copy of GNB3, weighs significantly more than its wild-type littermates, and has excess intraabdominal fat accumulation. GNB3 is highly expressed in the brain, consistent with G-protein signaling involved in satiety and/or metabolism. These functional data connect GNB3 duplication and overexpression to elevated body mass index and provide evidence for a genetic syndrome caused by a recurrent CNV.
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Affiliation(s)
- Ian S. Goldlust
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Karen E. Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Lisa M. Catalano
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Rebecca Cozad
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Grace Wynn
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Alev Cagla Ozdemir
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Karen N. Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Departments of Biostatistics and Bioinformatics and
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Epidemiology, Emory University School of Public Health, Atlanta, GA 30322
| | - Shikha Dharamrup
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Madhuri R. Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Katherine H. Kim
- Division of Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614
| | - Brad Angle
- Division of Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614
| | - Alison Colley
- Department of Clinical Genetics, South Western Sydney Local Health District, Liverpool, NSW 1871, Australia
| | - Amy E. Webb
- Amy E. Webb Pediatrics, Pismo Beach, CA 93449
| | - Erik C. Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Jay W. Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Jill A. Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Blake C. Ballif
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Lisa G. Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Laurie A. Demmer
- Division of Genetics and Metabolism, Tufts University School of Medicine, Boston, MA 02111; and
| | | | - M. Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
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28
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Golzio C, Katsanis N. Genetic architecture of reciprocal CNVs. Curr Opin Genet Dev 2013; 23:240-8. [PMID: 23747035 DOI: 10.1016/j.gde.2013.04.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/22/2013] [Accepted: 04/26/2013] [Indexed: 10/26/2022]
Abstract
Copy number variants (CNVs) represent a frequent type of lesion in human genetic disorders that typically affects numerous genes simultaneously. This has raised the challenge of understanding which genes within a CNV drive clinical phenotypes. Although CNVs can arise by multiple mechanisms, a subset is driven by local genomic architecture permissive to recombination events that can lead to both deletions and duplications. Phenotypic analyses of patients with such reciprocal CNVs have revealed instances in which the phenotype is either identical or mirrored; strikingly, molecular studies have shown that such phenotypes are often driven by reciprocal dosage defects of the same transcript. Here we explore how these observations can help the dissection of CNVs and inform the genetic architecture of CNV-induced disorders.
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Affiliation(s)
- Christelle Golzio
- Center for Human Disease Modeling, Duke University, Durham 27710, USA
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29
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Lacaria M, Gu W, Lupski JR. Circadian abnormalities in mouse models of Smith-Magenis syndrome: evidence for involvement of RAI1. Am J Med Genet A 2013; 161A:1561-8. [PMID: 23703963 DOI: 10.1002/ajmg.a.35941] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/22/2013] [Indexed: 11/06/2022]
Abstract
Smith-Magenis syndrome (SMS; OMIM 182290) is a genomic disorder characterized by multiple congenital anomalies, intellectual disability, behavioral abnormalities, and disordered sleep resulting from an ~3.7 Mb deletion copy number variant (CNV) on chromosome 17p11.2 or from point mutations in the gene RAI1. The reciprocal duplication of this region results in another genomic disorder, Potocki-Lupski syndrome (PTLS; OMIM 610883), characterized by autism, intellectual disability, and congenital anomalies. We previously used chromosome-engineering and gene targeting to generate mouse models for PTLS (Dp(11)17/+), and SMS due to either deletion CNV or gene knock-out (Df(11)17-2/+ and Rai1(+/-) , respectively) and we observed phenotypes in these mouse models consistent with their associated human syndromes. To investigate the contribution of individual genes to the circadian phenotypes observed in SMS, we now report the analysis of free-running period lengths in Rai1(+/-) and Df(11)17-2/+ mice, as well as in mice deficient for another known circadian gene mapping within the commonly deleted/duplicated region, Dexras1, and we compare these results to those previously observed in Dp(11)17/+ mice. Reduced free-running period lengths were seen in Df(11)17-2/+, Rai1(+/-) , and Dexras1(-/-) , but not Dexras1(+/-) mice, suggesting that Rai1 may be the primary gene underlying the circadian defects in SMS. However, we cannot rule out the possibility that cis effects between multiple haploinsufficient genes in the SMS critical interval (e.g., RAI1 and DEXRAS1) either exacerbate the circadian phenotypes observed in SMS patients with deletions or increase their penetrance in certain environments. This study also confirms a previous report of abnormal circadian function in Dexras1(-/-) mice.
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Affiliation(s)
- Melanie Lacaria
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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30
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Brunham LR, Hayden MR. Hunting human disease genes: lessons from the past, challenges for the future. Hum Genet 2013; 132:603-17. [PMID: 23504071 PMCID: PMC3654184 DOI: 10.1007/s00439-013-1286-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/23/2013] [Indexed: 12/30/2022]
Abstract
The concept that a specific alteration in an individual’s DNA can result in disease is central to our notion of molecular medicine. The molecular basis of more than 3,500 Mendelian disorders has now been identified. In contrast, the identification of genes for common disease has been much more challenging. We discuss historical and contemporary approaches to disease gene identification, focusing on novel opportunities such as the use of population extremes and the identification of rare variants. While our ability to sequence DNA has advanced dramatically, assigning function to a given sequence change remains a major challenge, highlighting the need for both bioinformatics and functional approaches to appropriately interpret these data. We review progress in mapping and identifying human disease genes and discuss future challenges and opportunities for the field.
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Affiliation(s)
- Liam R. Brunham
- Department of Medicine, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Translational Laboratory for Genetic Medicine, National University of Singapore and the Association for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Michael R. Hayden
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Translational Laboratory for Genetic Medicine, National University of Singapore and the Association for Science, Technology and Research (A*STAR), Singapore, Singapore
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31
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Pitcher MR, Ward CS, Arvide EM, Chapleau CA, Pozzo-Miller L, Hoeflich A, Sivaramakrishnan M, Saenger S, Metzger F, Neul JL. Insulinotropic treatments exacerbate metabolic syndrome in mice lacking MeCP2 function. Hum Mol Genet 2013; 22:2626-33. [PMID: 23462290 DOI: 10.1093/hmg/ddt111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rett syndrome (RTT), an X-linked postnatal disorder, results from mutations in Methyl CpG-binding protein 2 (MECP2). Survival and breathing in Mecp2(NULL/Y) animals are improved by an N-terminal tripeptide of insulin-like growth factor I (IGF-I) treatment. We determined that Mecp2(NULL/Y) animals also have a metabolic syndrome and investigated whether IGF-I treatment might improve this phenotype. Mecp2(NULL/Y) mice were treated with a full-length IGF-I modified with the addition of polyethylene glycol (PEG-IGF-I), which improves pharmacological properties. Low-dose PEG-IGF-I treatment slightly improved lifespan and heart rate in Mecp2(NULL/Y) mice; however, high-dose PEG-IGF-I decreased lifespan. To determine whether insulinotropic off-target effects of PEG-IGF-I caused the detrimental effect, we treated Mecp2(NULL/Y) mice with insulin, which also decreased lifespan. Thus, the clinical benefit of IGF-I treatment in RTT may critically depend on the dose used, and caution should be taken when initiating clinical trials with these compounds because the beneficial therapeutic window is narrow.
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Affiliation(s)
- Meagan R Pitcher
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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32
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Rosenfeld JA, Kim KH, Angle B, Troxell R, Gorski JL, Westemeyer M, Frydman M, Senturias Y, Earl D, Torchia B, Schultz RA, Ellison JW, Tsuchiya K, Zimmerman S, Smolarek TA, Ballif BC, Shaffer LG. Further Evidence of Contrasting Phenotypes Caused by Reciprocal Deletions and Duplications: Duplication of NSD1 Causes Growth Retardation and Microcephaly. Mol Syndromol 2013; 3:247-54. [PMID: 23599694 DOI: 10.1159/000345578] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2012] [Indexed: 12/15/2022] Open
Abstract
Microduplications of the Sotos syndrome region containing NSD1 on 5q35 have recently been proposed to cause a syndrome of microcephaly, short stature and developmental delay. To further characterize this emerging syndrome, we report the clinical details of 12 individuals from 8 families found to have interstitial duplications involving NSD1, ranging in size from 370 kb to 3.7 Mb. All individuals are microcephalic, and height and childhood weight range from below average to severely restricted. Mild-to-moderate learning disabilities and/or developmental delay are present in all individuals, including carrier family members of probands; dysmorphic features and digital anomalies are present in a majority. Craniosynostosis is present in the individual with the largest duplication, though the duplication does not include MSX2, mutations of which can cause craniosynostosis, on 5q35.2. A comparison of the smallest duplication in our cohort that includes the entire NSD1 gene to the individual with the largest duplication that only partially overlaps NSD1 suggests that whole-gene duplication of NSD1 in and of itself may be sufficient to cause the abnormal growth parameters seen in these patients. NSD1 duplications may therefore be added to a growing list of copy number variations for which deletion and duplication of specific genes have contrasting effects on body development.
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Affiliation(s)
- J A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Wash., USA
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33
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Lacaria M, Gu W, Lupski JR. A functional role for structural variation in metabolism. Adipocyte 2013; 2:55-57. [PMID: 23700554 PMCID: PMC3661138 DOI: 10.4161/adip.22031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A contribution of structural genomic variation to the heritability of complex metabolic phenotypes was illuminated by the recent characterization of chromosome-engineered mouse models for genomic disorders associated with metabolic dysfunction. Herein we discuss our study, "A duplication CNV that conveys traits reciprocal to metabolic syndrome and protects against diet-induced obesity in mice and men," which describes the opposing metabolic phenotypes of mouse models for two prototypical genomic disorders,1,2 Smith-Magenis syndrome (SMS) and Potocki-Lupski syndrome (PTLS). SMS and PTLS are caused by reciprocal deletion or duplication copy number variations (CNVs), respectively, on chromosome 17p11.2. The implications of the results of this study and the potential relevance of these findings for future studies in the field of metabolism are discussed.
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Affiliation(s)
- Melanie Lacaria
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston, TX USA
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34
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Heck DH, Gu W, Cao Y, Qi S, Lacaria M, Lupski JR. Opposing phenotypes in mice with Smith-Magenis deletion and Potocki-Lupski duplication syndromes suggest gene dosage effects on fluid consumption behavior. Am J Med Genet A 2012; 158A:2807-14. [PMID: 22991245 DOI: 10.1002/ajmg.a.35601] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 07/12/2012] [Indexed: 11/12/2022]
Abstract
A quantitative long-term fluid consumption and fluid-licking assay was performed in two mouse models with either an ∼2 Mb genomic deletion, Df(11)17, or the reciprocal duplication copy number variation (CNV), Dp(11)17, analogous to the human genomic rearrangements causing either Smith-Magenis syndrome [SMS; OMIM #182290] or Potocki-Lupski syndrome [PTLS; OMIM #610883], respectively. Both mouse strains display distinct quantitative alterations in fluid consumption compared to their wild-type littermates; several of these changes are diametrically opposing between the two chromosome engineered mouse models. Mice with duplication versus deletion showed longer versus shorter intervals between visits to the waterspout, generated more versus less licks per visit and had higher versus lower variability in the number of licks per lick-burst as compared to their respective wild-type littermates. These findings suggest that copy number variation can affect long-term fluid consumption behavior in mice. Other behavioral differences were unique for either the duplication or deletion mutants; the deletion CNV resulted in increased variability of the licking rhythm, and the duplication CNV resulted in a significant slowing of the licking rhythm. Our findings document a readily quantitated complex behavioral response that can be directly and reciprocally influenced by a gene dosage effect.
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Affiliation(s)
- Detlef H Heck
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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35
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Crespi B. Diametric gene-dosage effects as windows into neurogenetic architecture. Curr Opin Neurobiol 2012; 23:143-51. [PMID: 22995549 DOI: 10.1016/j.conb.2012.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/16/2012] [Accepted: 08/26/2012] [Indexed: 02/06/2023]
Abstract
Gene expression can be modulated in two opposite directions, towards higher or lower amounts of product. How do diametric changes in gene dosage influence neurological development and function? Recent studies of transgenic and knockout mouse models, genomic copy-number variants, imprinted-gene expression alterations, and sex-chromosome aneuploidies are revealing examples of 'mirror-extreme' brain and behavior phenotypes, which provide unique insights into neurodevelopmental architecture. These convergent studies quantitatively connect gene dosages with specific trajectories and outcomes, with important implications for the experimental dissection of normal neurological functions, the genetic analysis of psychiatric disorders, the development of pharmacological therapies, and mechanisms for the evolution of human brain and behavior.
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Affiliation(s)
- Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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