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Liang F, Wang B, Geng J, You G, Fa J, Zhang M, Sun H, Chen H, Fu Q, Zhang X, Zhang Z. SORBS2 is a genetic factor contributing to cardiac malformation of 4q deletion syndrome patients. eLife 2021; 10:e67481. [PMID: 34099102 PMCID: PMC8186900 DOI: 10.7554/elife.67481] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/16/2021] [Indexed: 11/15/2022] Open
Abstract
Chromosome 4q deletion is one of the most frequently detected genomic imbalance events in congenital heart disease (CHD) patients. However, a portion of CHD-associated 4q deletions without known CHD genes suggests unknown CHD genes within these intervals. Here, we have shown that knockdown of SORBS2, a 4q interval gene, disrupted sarcomeric integrity of cardiomyocytes and caused reduced cardiomyocyte number in human embryonic stem cell differentiation model. Molecular analyses revealed decreased expression of second heart field (SHF) marker genes and impaired NOTCH and SHH signaling in SORBS2-knockdown cells. Exogenous SHH rescued SORBS2 knockdown-induced cardiomyocyte differentiation defects. Sorbs2-/- mouse mutants had atrial septal hypoplasia/aplasia or double atrial septum (DAS) derived from impaired posterior SHF with a similar expression alteration. Rare SORBS2 variants were significantly enriched in a cohort of 300 CHD patients. Our findings indicate that SORBS2 is a regulator of SHF development and its variants contribute to CHD pathogenesis. The presence of DAS in Sorbs2-/- hearts reveals the first molecular etiology of this rare anomaly linked to paradoxical thromboembolism.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Adolescent
- Animals
- Case-Control Studies
- Cell Differentiation
- Child
- Child, Preschool
- Chromosome Deletion
- Chromosome Disorders/diagnosis
- Chromosome Disorders/genetics
- Chromosomes, Human, Pair 4/genetics
- Databases, Genetic
- Female
- Gene Expression Regulation, Developmental
- Genetic Predisposition to Disease
- HEK293 Cells
- Heart Defects, Congenital/diagnosis
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/metabolism
- Hedgehog Proteins/genetics
- Hedgehog Proteins/metabolism
- Human Embryonic Stem Cells/metabolism
- Human Embryonic Stem Cells/pathology
- Humans
- Infant
- Infant, Newborn
- Male
- Mice, Inbred C57BL
- Mice, Knockout
- Mutation
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Phenotype
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Notch/genetics
- Receptors, Notch/metabolism
- Signal Transduction
- Mice
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Affiliation(s)
- Fei Liang
- Neonatal Intensive Care Unit, Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Bo Wang
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Juan Geng
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Guoling You
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jingjing Fa
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Min Zhang
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hunying Sun
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health and Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Huiwen Chen
- Department of thoracic and cardiac surgery, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Qihua Fu
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaoqing Zhang
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhen Zhang
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of MedicineShanghaiChina
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2
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Cytogenomic Evaluation of Subjects with Syndromic and Nonsyndromic Conotruncal Heart Defects. BIOMED RESEARCH INTERNATIONAL 2015; 2015:401941. [PMID: 26137477 PMCID: PMC4475533 DOI: 10.1155/2015/401941] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/01/2015] [Accepted: 05/03/2015] [Indexed: 02/07/2023]
Abstract
Despite considerable advances in the detection of genomic abnormalities in congenital heart disease (CHD), the etiology of CHD remains largely unknown. CHD is the most common birth defect and is a major cause of infant morbidity and mortality, and conotruncal defects constitute 20% of all CHD cases. We used array comparative genomic hybridization (array-CGH) to retrospectively study 60 subjects with conotruncal defects and identify genomic imbalances. The DNA copy number variations (CNVs) detected were matched with data from genomic databases, and their clinical significance was evaluated. We found that 38.3% (23/60) of CHD cases possessed genomic imbalances. In 8.3% (5/60) of these cases, the imbalances were causal or potentially causal CNVs; in 8.3% (5/60), unclassified CNVs were identified; and in 21.6% (13/60), common variants were detected. Although the interpretation of the results must be refined and there is not yet a consensus regarding the types of CHD cases in which array-CGH should be used as a first-line test, the identification of these CNVs can assist in the evaluation and management of CHD. The results of such studies emphasize the growing importance of the use of genome-wide assays in subjects with CHD to increase the number of genomic data sets associated with this condition.
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Moosmann J, Uebe S, Dittrich S, Rüffer A, Ekici AB, Toka O. Novel loci for non-syndromic coarctation of the aorta in sporadic and familial cases. PLoS One 2015; 10:e0126873. [PMID: 25984793 PMCID: PMC4436177 DOI: 10.1371/journal.pone.0126873] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/08/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Coarctation of the aorta (CoA) accounts for 5-8% of all congenital heart defects. CoA can be detected in up to 20% of patients with Ullrich-Turner syndrome (UTS), in which a part or all of one of the X chromosomes is absent. The etiology of non-syndromic CoA is poorly understood. In the present work, we test the hypothesis that rare copy number variation (CNV) especially on the gonosomes, contribute to the etiology of non-syndromic CoA. METHODS We performed high-resolution genome-wide CNV analysis using the Affymetrix SNP 6.0 microarray platform for 70 individuals with sporadic CoA, 3 families with inherited CoA (n=13) and 605 controls. Our analysis comprised genome wide association, CNV burden and linkage. CNV was validated by multiplex ligation-dependent probe amplification. RESULTS We identified a significant abundance of large (>100 kb) CNVs on the X chromosome in males with CoA (p=0.005). 11 out of 51 (~ 22%) male cases had these large CNVs. Association analysis in the sporadic cohort revealed 14 novel loci for CoA. The locus on 21q22.3 in the sporadic CoA cohort overlapped with a gene locus identified in all familial cases of CoA (candidate gene TRPM2). We identified one CNV locus within a locus with high multipoint LOD score from a linkage analysis of the familial cases (SEPT9); another locus overlapped with a region implicated in Kabuki syndrome. In the familial cases, we identified a total of 7 CNV loci that were exclusively present in cases but not in unaffected family members. CONCLUSION Of all candidate loci identified, the TRPM2 locus was the most frequently implicated autosomal locus in sporadic and familial cases. However, the abundance of large CNVs on the X chromosome of affected males suggests that gonosomal aberrations are not only responsible for syndromic CoA but also involved in the development of sporadic and non-syndromic CoA and their male dominance.
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Affiliation(s)
- Julia Moosmann
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiology, Loschgestraße 15, 91054 Erlangen, Germany
| | - Steffen Uebe
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Sven Dittrich
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiology, Loschgestraße 15, 91054 Erlangen, Germany
| | - André Rüffer
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiac Surgery, Loschgestraße 15, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Okan Toka
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Department of Pediatric Cardiology, Loschgestraße 15, 91054 Erlangen, Germany
- * E-mail:
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Jia Y, Louw JJ, Breckpot J, Callewaert B, Barrea C, Sznajer Y, Gewillig M, Souche E, Dehaspe L, Vermeesch JR, Lambrechts D, Devriendt K, Corveleyn A. The diagnostic value of next generation sequencing in familial nonsyndromic congenital heart defects. Am J Med Genet A 2015; 167A:1822-9. [DOI: 10.1002/ajmg.a.37108] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/19/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Yaojuan Jia
- Department of Human Genetics; KU Leuven; Leuven Belgium
| | - Jacoba J. Louw
- Department of Human Genetics; KU Leuven; Leuven Belgium
- Department of Congenital and Pediatric Cardiology; University Hospitals Leuven; Leuven Belgium
| | - Jeroen Breckpot
- Department of Human Genetics; KU Leuven; Leuven Belgium
- Department of Pediatrics; University Hospitals Leuven; Leuven Belgium
| | - Bert Callewaert
- Center for Medical Genetics; University of Ghent; Ghent Belgium
| | - Catherine Barrea
- Department of Congenital and Pediatric Cardiology; Universit; é; Catholique de Louvain; Brussels Belgium
| | - Yves Sznajer
- Center for Human Genetics; Université Catholique de Louvain; Brussels Belgium
| | - Marc Gewillig
- Department of Congenital and Pediatric Cardiology; University Hospitals Leuven; Leuven Belgium
| | - Erika Souche
- Department of Human Genetics; KU Leuven; Leuven Belgium
| | - Luc Dehaspe
- Department of Human Genetics; KU Leuven; Leuven Belgium
| | | | - Diether Lambrechts
- Department of Oncology; KU Leuven; Leuven Belgium
- Vesalius Research Center; VIB; Leuven Belgium
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5
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Decoding the complex genetic causes of heart diseases using systems biology. Biophys Rev 2015; 7:141-159. [PMID: 28509974 DOI: 10.1007/s12551-014-0145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022] Open
Abstract
The pace of disease gene discovery is still much slower than expected, even with the use of cost-effective DNA sequencing and genotyping technologies. It is increasingly clear that many inherited heart diseases have a more complex polygenic aetiology than previously thought. Understanding the role of gene-gene interactions, epigenetics, and non-coding regulatory regions is becoming increasingly critical in predicting the functional consequences of genetic mutations identified by genome-wide association studies and whole-genome or exome sequencing. A systems biology approach is now being widely employed to systematically discover genes that are involved in heart diseases in humans or relevant animal models through bioinformatics. The overarching premise is that the integration of high-quality causal gene regulatory networks (GRNs), genomics, epigenomics, transcriptomics and other genome-wide data will greatly accelerate the discovery of the complex genetic causes of congenital and complex heart diseases. This review summarises state-of-the-art genomic and bioinformatics techniques that are used in accelerating the pace of disease gene discovery in heart diseases. Accompanying this review, we provide an interactive web-resource for systems biology analysis of mammalian heart development and diseases, CardiacCode ( http://CardiacCode.victorchang.edu.au/ ). CardiacCode features a dataset of over 700 pieces of manually curated genetic or molecular perturbation data, which enables the inference of a cardiac-specific GRN of 280 regulatory relationships between 33 regulator genes and 129 target genes. We believe this growing resource will fill an urgent unmet need to fully realise the true potential of predictive and personalised genomic medicine in tackling human heart disease.
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6
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Li X, Martinez-Fernandez A, Hartjes KA, Kocher JPA, Olson TM, Terzic A, Nelson TJ. Transcriptional atlas of cardiogenesis maps congenital heart disease interactome. Physiol Genomics 2014; 46:482-95. [PMID: 24803680 DOI: 10.1152/physiolgenomics.00015.2014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease.
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Affiliation(s)
- Xing Li
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | | | - Katherine A Hartjes
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Jean-Pierre A Kocher
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Timothy M Olson
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota; Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota; Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Andre Terzic
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota; Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Timothy J Nelson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota; Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota; Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota; Transplant Center, Mayo Clinic, Rochester, Minnesota; and Division of General Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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7
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Lalani SR, Belmont JW. Genetic basis of congenital cardiovascular malformations. Eur J Med Genet 2014; 57:402-13. [PMID: 24793338 DOI: 10.1016/j.ejmg.2014.04.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/16/2014] [Indexed: 01/14/2023]
Abstract
Cardiovascular malformations are a singularly important class of birth defects and due to dramatic improvements in medical and surgical care, there are now large numbers of adult survivors. The etiologies are complex, but there is strong evidence that genetic factors play a crucial role. Over the last 15 years there has been enormous progress in the discovery of causative genes for syndromic heart malformations and in rare families with Mendelian forms. The rapid characterization of genomic disorders as major contributors to congenital heart defects is also notable. The genes identified encode many transcription factors, chromatin regulators, growth factors and signal transduction proteins- all unified by their required roles in normal cardiac development. Genome-wide sequencing of the coding regions promises to elucidate genetic causation in several disorders affecting cardiac development. Such comprehensive studies evaluating both common and rare variants would be essential in characterizing gene-gene interactions, as well as in understanding the gene-environment interactions that increase susceptibility to congenital heart defects.
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Affiliation(s)
- Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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8
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Thorsson T, Russell WW, El-Kashlan N, Soemedi R, Levine J, Geisler SB, Ackley T, Tomita-Mitchell A, Rosenfeld JA, Töpf A, Tayeh M, Goodship J, Innis JW, Keavney B, Russell MW. Chromosomal Imbalances in Patients with Congenital Cardiac Defects: A Meta-analysis Reveals Novel Potential Critical Regions Involved in Heart Development. CONGENIT HEART DIS 2014; 10:193-208. [PMID: 24720490 DOI: 10.1111/chd.12179] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2014] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Congenital cardiac defects represent the most common group of birth defects, affecting an estimated six per 1000 births. Genetic characterization of patients and families with cardiac defects has identified a number of genes required for heart development. Yet, despite the rapid pace of these advances, mutations affecting known genes still account for only a small fraction of congenital heart defects suggesting that many more genes and developmental mechanisms remain to be identified. DESIGN In this study, we reviewed 1694 described cases of patients with cardiac defects who were determined to have a significant chromosomal imbalance (a deletion or duplication). The cases were collected from publicly available databases (DECIPHER, ISCA, and CHDWiki) and from recent publications. An additional 68 nonredundant cases were included from the University of Michigan. Cases with multiple chromosomal or whole chromosome defects (trisomy 13, 18, 21) were excluded, and cases with overlapping deletions and/or insertions were grouped to identify regions potentially involved in heart development. RESULTS Seventy-nine chromosomal regions were identified in which 5 or more patients had overlapping imbalances. Regions of overlap were used to determine minimal critical domains most likely to contain genes or regulatory elements involved in heart development. This approach was used to refine the critical regions responsible for cardiac defects associated with chromosomal imbalances involving 1q24.2, 2q31.1, 15q26.3, and 22q11.2. CONCLUSIONS The pattern of chromosomal imbalances in patients with congenital cardiac defects suggests that many loci may be involved in normal heart development, some with very strong and direct effects and others with less direct effects. Chromosomal duplication/deletion mapping will provide an important roadmap for genome-wide sequencing and genetic mapping strategies to identify novel genes critical for heart development.
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Affiliation(s)
- Thor Thorsson
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Mich, USA
| | - William W Russell
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Mich, USA
| | - Nour El-Kashlan
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Mich, USA
| | - Rachel Soemedi
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Jonathan Levine
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Mich, USA
| | - Sarah B Geisler
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Mich, USA
| | - Todd Ackley
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, University of Michigan, Ann Arbor, Mich, USA
| | | | - Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Wash, USA
| | - Ana Töpf
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marwan Tayeh
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, University of Michigan, Ann Arbor, Mich, USA
| | - Judith Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeffrey W Innis
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Genetics, University of Michigan, Ann Arbor, Mich, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Mich, USA
| | - Bernard Keavney
- Institute of Cardiovascular Sciences, Central Manchester University, Manchester, United Kingdom
| | - Mark W Russell
- Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan, Ann Arbor, Mich, USA
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9
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Al Turki S, Manickaraj A, Mercer C, Gerety S, Hitz MP, Lindsay S, D’Alessandro L, Swaminathan G, Bentham J, Arndt AK, Louw J, Breckpot J, Gewillig M, Thienpont B, Abdul-Khaliq H, Harnack C, Hoff K, Kramer HH, Schubert S, Siebert R, Toka O, Cosgrove C, Watkins H, Lucassen A, O’Kelly I, Salmon A, Bu’Lock F, Granados-Riveron J, Setchfield K, Thornborough C, Brook J, Mulder B, Klaassen S, Bhattacharya S, Devriendt K, FitzPatrick D, Wilson D, Mital S, Hurles M, Mital S, Hurles ME. Rare variants in NR2F2 cause congenital heart defects in humans. Am J Hum Genet 2014; 94:574-85. [PMID: 24702954 DOI: 10.1016/j.ajhg.2014.03.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/12/2014] [Indexed: 11/25/2022] Open
Abstract
Congenital heart defects (CHDs) are the most common birth defect worldwide and are a leading cause of neonatal mortality. Nonsyndromic atrioventricular septal defects (AVSDs) are an important subtype of CHDs for which the genetic architecture is poorly understood. We performed exome sequencing in 13 parent-offspring trios and 112 unrelated individuals with nonsyndromic AVSDs and identified five rare missense variants (two of which arose de novo) in the highly conserved gene NR2F2, a very significant enrichment (p = 7.7 × 10(-7)) compared to 5,194 control subjects. We identified three additional CHD-affected families with other variants in NR2F2 including a de novo balanced chromosomal translocation, a de novo substitution disrupting a splice donor site, and a 3 bp duplication that cosegregated in a multiplex family. NR2F2 encodes a pleiotropic developmental transcription factor, and decreased dosage of NR2F2 in mice has been shown to result in abnormal development of atrioventricular septa. Via luciferase assays, we showed that all six coding sequence variants observed in individuals significantly alter the activity of NR2F2 on target promoters.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Seema Mital
- Division of Cardiology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada.
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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10
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Osoegawa K, Iovannisci DM, Lin B, Parodi C, Schultz K, Shaw GM, Lammer EJ. Identification of novel candidate gene loci and increased sex chromosome aneuploidy among infants with conotruncal heart defects. Am J Med Genet A 2013; 164A:397-406. [PMID: 24127225 DOI: 10.1002/ajmg.a.36291] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 09/10/2013] [Indexed: 12/17/2022]
Abstract
Congenital heart defects (CHDs) are common malformations, affecting four to eight per 1,000 total births. Conotruncal defects are an important pathogenetic subset of CHDs, comprising nearly 20% of the total. Although both environmental and genetic factors are known to contribute to the occurrence of conotruncal defects, the causes remain unknown for most. To identify novel candidate genes/loci, we used array comparative genomic hybridization to detect chromosomal microdeletions/duplications. From a population base of 974,579 total births born during 1999-2004, we screened 389 California infants born with tetralogy of Fallot or d-transposition of the great arteries. We found that 1.7% (5/288) of males with a conotruncal defect had sex chromosome aneuploidy, a sevenfold increased frequency (relative risk = 7.0; 95% confidence interval 2.9-16.9). We identified eight chromosomal microdeletions/duplications for conotruncal defects. From these duplications and deletions, we found five high priority candidate genes (GATA4, CRKL, BMPR1A, SNAI2, and ZFHX4). This is the initial report that sex chromosome aneuploidy is associated with conotruncal defects among boys. These chromosomal microduplications/deletions provide evidence that GATA4, SNAI2, and CRKL are highly dosage sensitive genes involved in outflow tract development. Genome wide screening for copy number variation can be productive for identifying novel genes/loci contributing to non-syndromic common malformations.
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Affiliation(s)
- Kazutoyo Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland, Oakland, California
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11
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Dorn C, Grunert M, Sperling SR. Application of high-throughput sequencing for studying genomic variations in congenital heart disease. Brief Funct Genomics 2013; 13:51-65. [PMID: 24095982 DOI: 10.1093/bfgp/elt040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Congenital heart diseases (CHD) represent the most common birth defect in human. The majority of cases are caused by a combination of complex genetic alterations and environmental influences. In the past, many disease-causing mutations have been identified; however, there is still a large proportion of cardiac malformations with unknown precise origin. High-throughput sequencing technologies established during the last years offer novel opportunities to further study the genetic background underlying the disease. In this review, we provide a roadmap for designing and analyzing high-throughput sequencing studies focused on CHD, but also with general applicability to other complex diseases. The three main next-generation sequencing (NGS) platforms including their particular advantages and disadvantages are presented. To identify potentially disease-related genomic variations and genes, different filtering steps and gene prioritization strategies are discussed. In addition, available control datasets based on NGS are summarized. Finally, we provide an overview of current studies already using NGS technologies and showing that these techniques will help to further unravel the complex genetics underlying CHD.
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Affiliation(s)
- Cornelia Dorn
- Department of Cardiovascular Genetics, Experimental and Clinical Research Center (ECRC), Charité-University Medicine Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany. Department of Biochemistry, Free University Berlin, Berlin, Germany. Tel.: +49-(0)30-450540123; Fax: +49-(0)30-84131699;
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12
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Gould RA, Aboulmouna LM, Varner JD, Butcher JT. Hierarchical approaches for systems modeling in cardiac development. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:289-305. [PMID: 23463736 DOI: 10.1002/wsbm.1217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ordered cardiac morphogenesis and function are essential for all vertebrate life. The heart begins as a simple contractile tube, but quickly grows and morphs into a multichambered pumping organ complete with valves, while maintaining regulation of blood flow and nutrient distribution. Though not identical, cardiac morphogenesis shares many molecular and morphological processes across vertebrate species. Quantitative data across multiple time and length scales have been gathered through decades of reductionist single variable analyses. These range from detailed molecular signaling pathways at the cellular levels to cardiac function at the tissue/organ levels. However, none of these components act in true isolation from others, and each, in turn, exhibits short- and long-range effects in both time and space. With the absence of a gene, entire signaling cascades and genetic profiles may be shifted, resulting in complex feedback mechanisms. Also taking into account local microenvironmental changes throughout development, it is apparent that a systems level approach is an essential resource to accelerate information generation concerning the functional relationships across multiple length scales (molecular data vs physiological function) and structural development. In this review, we discuss relevant in vivo and in vitro experimental approaches, compare different computational frameworks for systems modeling, and the latest information about systems modeling of cardiac development. Finally, we conclude with some important future directions for cardiac systems modeling.
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Affiliation(s)
- Russell A Gould
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet 2012; 13:523-36. [DOI: 10.1038/nrg3253] [Citation(s) in RCA: 332] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Breckpot J, Thienpont B, Bauters M, Tranchevent LC, Gewillig M, Allegaert K, Vermeesch JR, Moreau Y, Devriendt K. Congenital heart defects in a novel recurrent 22q11.2 deletion harboring the genes CRKL and MAPK1. Am J Med Genet A 2012; 158A:574-80. [DOI: 10.1002/ajmg.a.35217] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 12/07/2011] [Indexed: 01/08/2023]
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Tomita-Mitchell A, Mahnke DK, Struble CA, Tuffnell ME, Stamm KD, Hidestrand M, Harris SE, Goetsch MA, Simpson PM, Bick DP, Broeckel U, Pelech AN, Tweddell JS, Mitchell ME. Human gene copy number spectra analysis in congenital heart malformations. Physiol Genomics 2012; 44:518-41. [PMID: 22318994 DOI: 10.1152/physiolgenomics.00013.2012] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The clinical significance of copy number variants (CNVs) in congenital heart disease (CHD) continues to be a challenge. Although CNVs including genes can confer disease risk, relationships between gene dosage and phenotype are still being defined. Our goal was to perform a quantitative analysis of CNVs involving 100 well-defined CHD risk genes identified through previously published human association studies in subjects with anatomically defined cardiac malformations. A novel analytical approach permitting CNV gene frequency "spectra" to be computed over prespecified regions to determine phenotype-gene dosage relationships was employed. CNVs in subjects with CHD (n = 945), subphenotyped into 40 groups and verified in accordance with the European Paediatric Cardiac Code, were compared with two control groups, a disease-free cohort (n = 2,026) and a population with coronary artery disease (n = 880). Gains (≥200 kb) and losses (≥100 kb) were determined over 100 CHD risk genes and compared using a Barnard exact test. Six subphenotypes showed significant enrichment (P ≤ 0.05), including aortic stenosis (valvar), atrioventricular canal (partial), atrioventricular septal defect with tetralogy of Fallot, subaortic stenosis, tetralogy of Fallot, and truncus arteriosus. Furthermore, CNV gene frequency spectra were enriched (P ≤ 0.05) for losses at: FKBP6, ELN, GTF2IRD1, GATA4, CRKL, TBX1, ATRX, GPC3, BCOR, ZIC3, FLNA and MID1; and gains at: PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, HRAS, GATA6 and RUNX1. Of CHD subjects, 14% had causal chromosomal abnormalities, and 4.3% had likely causal (significantly enriched), large, rare CNVs. CNV frequency spectra combined with precision phenotyping may lead to increased molecular understanding of etiologic pathways.
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Affiliation(s)
- Aoy Tomita-Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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Abstract
A review of 2010 research in translational bioinformatics provides much to marvel at. We have seen notable advances in personal genomics, pharmacogenetics, and sequencing. At the same time, the infrastructure for the field has burgeoned. While acknowledging that, according to researchers, the members of this field tend to be overly optimistic, the authors predict a bright future.
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Affiliation(s)
- Russ B Altman
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California 94305-5444, USA.
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Breckpot J, Thienpont B, Arens Y, Tranchevent L, Vermeesch J, Moreau Y, Gewillig M, Devriendt K. Challenges of Interpreting Copy Number Variation in Syndromic and Non-Syndromic Congenital Heart Defects. Cytogenet Genome Res 2011; 135:251-9. [DOI: 10.1159/000331272] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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YTPdb: A wiki database of yeast membrane transporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1908-12. [DOI: 10.1016/j.bbamem.2010.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 05/17/2010] [Accepted: 06/07/2010] [Indexed: 02/04/2023]
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Brohée S, Barriot R, Moreau Y. Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases. ACTA ACUST UNITED AC 2010; 26:2210-1. [PMID: 20591906 DOI: 10.1093/bioinformatics/btq348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SUMMARY In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. AVAILABILITY The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.
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Affiliation(s)
- Sylvain Brohée
- ESAT-SCD. Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium.
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Thienpont B, Zhang L, Postma AV, Breckpot J, Tranchevent LC, Van Loo P, Møllgård K, Tommerup N, Bache I, Tümer Z, van Engelen K, Menten B, Mortier G, Waggoner D, Gewillig M, Moreau Y, Devriendt K, Larsen LA. Haploinsufficiency of TAB2 causes congenital heart defects in humans. Am J Hum Genet 2010; 86:839-49. [PMID: 20493459 DOI: 10.1016/j.ajhg.2010.04.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 04/12/2010] [Accepted: 04/20/2010] [Indexed: 01/20/2023] Open
Abstract
Congenital heart defects (CHDs) are the most common major developmental anomalies and the most frequent cause for perinatal mortality, but their etiology remains often obscure. We identified a locus for CHDs on 6q24-q25. Genotype-phenotype correlations in 12 patients carrying a chromosomal deletion on 6q delineated a critical 850 kb region on 6q25.1 harboring five genes. Bioinformatics prioritization of candidate genes in this locus for a role in CHDs identified the TGF-beta-activated kinase 1/MAP3K7 binding protein 2 gene (TAB2) as the top-ranking candidate gene. A role for this candidate gene in cardiac development was further supported by its conserved expression in the developing human and zebrafish heart. Moreover, a critical, dosage-sensitive role during development was demonstrated by the cardiac defects observed upon titrated knockdown of tab2 expression in zebrafish embryos. To definitively confirm the role of this candidate gene in CHDs, we performed mutation analysis of TAB2 in 402 patients with a CHD, which revealed two evolutionarily conserved missense mutations. Finally, a balanced translocation was identified, cosegregating with familial CHD. Mapping of the breakpoints demonstrated that this translocation disrupts TAB2. Taken together, these data clearly demonstrate a role for TAB2 in human cardiac development.
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