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Carlisle SG, Albasha H, Michelena HI, Sabate-Rotes A, Bianco L, De Backer J, Mosquera LM, Yetman AT, Bissell MM, Andreassi MG, Foffa I, Hui DS, Caffarelli A, Kim YY, Guo D, Citro R, De Marco M, Tretter JT, McBride KL, Milewicz DM, Body SC, Prakash SK. Rare genomic copy number variants implicate new candidate genes for bicuspid aortic valve. PLoS One 2024; 19:e0304514. [PMID: 39240962 PMCID: PMC11379187 DOI: 10.1371/journal.pone.0304514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/14/2024] [Indexed: 09/08/2024] Open
Abstract
Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in a BAV cohort with late onset sporadic disease (n = 5040). We identified 3 large and rare (< 1,1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting with GATA4 and DSCAM were enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 9% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.
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Affiliation(s)
- Steven G Carlisle
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Hasan Albasha
- University College Dublin School of Medicine, Dublin, Ireland
| | | | | | - Lisa Bianco
- Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Anji T Yetman
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | | | | | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dawn S Hui
- University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Anthony Caffarelli
- Hoag Memorial Hospital Presbyterian, Newport Beach, California, United States of America
| | - Yuli Y Kim
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dongchuan Guo
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Rodolfo Citro
- University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | | | - Kim L McBride
- University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
| | - Dianna M Milewicz
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Simon C Body
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Siddharth K Prakash
- University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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2
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Genetics and Molecular Basis of Congenital Heart Defects in Down Syndrome: Role of Extracellular Matrix Regulation. Int J Mol Sci 2023; 24:ijms24032918. [PMID: 36769235 PMCID: PMC9918028 DOI: 10.3390/ijms24032918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Down syndrome (DS), a complex disorder that is caused by the trisomy of chromosome 21 (Hsa21), is a major cause of congenital heart defects (CHD). Interestingly, only about 50% of individuals with Hsa21 trisomy manifest CHD. Here we review the genetic basis of CHD in DS, focusing on genes that regulate extracellular matrix (ECM) organization. The overexpression of Hsa21 genes likely underlies the molecular mechanisms that contribute to CHD, even though the genes responsible for CHD could only be located in a critical region of Hsa21. A role in causing CHD has been attributed not only to protein-coding Hsa21 genes, but also to genes on other chromosomes, as well as miRNAs and lncRNAs. It is likely that the contribution of more than one gene is required, and that the overexpression of Hsa21 genes acts in combination with other genetic events, such as specific mutations or polymorphisms, amplifying their effect. Moreover, a key function in determining alterations in cardiac morphogenesis might be played by ECM. A large number of genes encoding ECM proteins are overexpressed in trisomic human fetal hearts, and many of them appear to be under the control of a Hsa21 gene, the RUNX1 transcription factor.
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3
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Congenital heart defects among Down’s syndrome cases: an updated review from basic research to an emerging diagnostics technology and genetic counselling. J Genet 2021. [DOI: 10.1007/s12041-021-01296-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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4
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Zhang H, Liu L, Tian J. Molecular mechanisms of congenital heart disease in down syndrome. Genes Dis 2019; 6:372-377. [PMID: 31832516 PMCID: PMC6889238 DOI: 10.1016/j.gendis.2019.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 12/31/2022] Open
Abstract
Down syndrome (DS), as a typical genomic aneuploidy, is a common cause of various birth defects, among which is congenital heart disease (CHD). 40-60% neonates with DS have some kinds of CHD. However, the molecular pathogenic mechanisms of DS associated CHD are still not fully understood. This review summarizes available studies on DS associated CHD from seven aspects so as to provide a crucial and updated overview of what we known so far in this domain.
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Affiliation(s)
- Hui Zhang
- Department of Cardiology, Heart Centre, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Lingjuan Liu
- Department of Cardiology, Heart Centre, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Jie Tian
- Department of Cardiology, Heart Centre, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
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5
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Genotype-phenotype correlation for congenital heart disease in Down syndrome through analysis of partial trisomy 21 cases. Genomics 2017. [PMID: 28648597 DOI: 10.1016/j.ygeno.2017.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Among Down syndrome (DS) children, 40-50% have congenital heart disease (CHD). Although trisomy 21 is not sufficient to cause CHD, three copies of at least part of chromosome 21 (Hsa21) increases the risk for CHD. In order to establish a genotype-phenotype correlation for CHD in DS, we built an integrated Hsa21 map of all described partial trisomy 21 (PT21) cases with sufficient indications regarding presence or absence of CHD (n=107), focusing on DS PT21 cases. We suggest a DS CHD candidate region on 21q22.2 (0.96Mb), being shared by most PT21 cases with CHD and containing three known protein-coding genes (DSCAM, BACE2, PLAC4) and four known non-coding RNAs (DSCAM-AS1, DSCAM-IT1, LINC00323, MIR3197). The characterization of a DS CHD candidate region provides a useful approach to identify specific genes contributing to the pathology and to orient further investigations and possibly more effective therapy in relation to the multifactorial pathogenesis of CHD.
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6
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Glidewell SC, Miyamoto SD, Grossfeld PD, Clouthier DE, Coldren CD, Stearman RS, Geraci MW. Transcriptional Impact of Rare and Private Copy Number Variants in Hypoplastic Left Heart Syndrome. Clin Transl Sci 2015; 8:682-9. [PMID: 26534787 DOI: 10.1111/cts.12340] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Hypoplastic left heart syndrome (HLHS) is a heterogeneous, lethal combination of congenital malformations characterized by severe underdevelopment of left heart structures, resulting in a univentricular circulation. The genetic determinants of this disorder are largely unknown. Evidence of copy number variants (CNVs) contributing to the genetic etiology of HLHS and other congenital heart defects has been mounting. However, the functional effects of such CNVs have not been examined, particularly in cases where the variant of interest is found in only a single patient. METHODS AND RESULTS Whole-genome SNP microarrays were employed to detect CNVs in two patient cohorts (N = 70 total) predominantly diagnosed with some form of nonsyndromic HLHS. We discovered 16 rare or private variants adjacent to or overlapping 20 genes associated with cardiovascular or premature lethality phenotypes in mouse knockout models. We evaluated the impact of selected variants on the expression of nine of these genes through quantitative PCR on cDNA derived from patient heart tissue. Four genes displayed significantly altered expression in patients with an overlapping or proximal CNV verses patients without such CNVs. CONCLUSION Rare and private genomic imbalances perturb transcription of genes that potentially affect cardiogenesis in a subset of nonsyndromic HLHS patients.
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Affiliation(s)
- Steven C Glidewell
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Shelley D Miyamoto
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Department of Pediatrics, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Paul D Grossfeld
- Department of Pediatrics, University of California, San Diego, California, USA
| | - David E Clouthier
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Robert S Stearman
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mark W Geraci
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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7
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Roles for DSCAM and DSCAML1 in central nervous system development and disease. ADVANCES IN NEUROBIOLOGY 2014; 8:249-70. [PMID: 25300140 DOI: 10.1007/978-1-4614-8090-7_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DSCAMs (Down syndrome cell adhesion molecules) are a group of immunoglobulin-like transmembrane proteins that contain fibronectin III domains. The founding member of the family was isolated in a positional cloning study that sought to identify genes located on chromosome 21 at the locus 21q22.2-q22.3 that is implicated in the neurological and cardiac phenotypes associated with Down's syndrome. In Drosophila, Dscam proteins are involved in neuronal wiring, while in vertebrates, the role of these cell adhesion molecules in neurogenesis, dendritogenesis, axonal outgrowth, synaptogenesis, and synaptic plasticity is only just beginning to be understood. In this chapter, we will review the functions ascribed to the two paralogous proteins found in humans, DSCAM and DSCAML1 (DSCAM-like 1), based on findings in knockout mice. The signaling pathways downstream of DSCAM activation and the role of DSCAM miss-expression in disease will be also discussed, particularly with regard to the intellectual disability in Down's syndrome.
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8
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Cetin Z, Yakut S, Mihci E, Manguoglu AE, Berker S, Keser I, Luleci G. A patient with Down syndrome with a de novo derivative chromosome 21. Gene 2012; 507:159-64. [PMID: 22827956 DOI: 10.1016/j.gene.2012.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 07/02/2012] [Accepted: 07/12/2012] [Indexed: 11/16/2022]
Abstract
Pure partial trisomy of chromosome 21 is a rare event. The patients with this aberration are very important for setting up precise karyotype-phenotype correlations particularly in Down syndrome phenotype. We present here a patient with Down syndrome with a de novo derivative chromosome 21. Karyotype of the patient was designated as 46,XY,der(21)(p13)dup(21)(q11.2q21.3)dup(21)(q22.2q22.3) with regard to cytogenetic, FISH and array-CGH analyses. Non-continuous monosomic, disomic and trisomic chromosomal segments through the derivative chromosome 21 were detected by array-CGH analysis. STR analyses revealed maternal origin of the de novo derivative chromosome 21. The dual-specificity tyrosine (Y)-phosphorylation regulated kinase 1A (DYRK1A) and Down Syndrome Critical Region 1 (DSCR1) genes that are located in Down syndrome critical region, are supposed to be responsible for most of the clinical findings of Down syndrome. However, our patient is the first patient with Down syndrome whose clinical findings were provided in detail, with a de novo derivative chromosome 21 resulting from multiple chromosome breaks excluding DYRK1A and DSCR1 gene regions.
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Affiliation(s)
- Zafer Cetin
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
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9
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A de novo duplication of chromosome 21q22.11→qter associated with Down syndrome: Prenatal diagnosis, molecular cytogenetic characterization and fetal ultrasound findings. Taiwan J Obstet Gynecol 2011; 50:492-8. [DOI: 10.1016/j.tjog.2011.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2010] [Indexed: 11/22/2022] Open
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10
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Vaglio A, Milunsky A, Quadrelli A, Huang XL, Maher T, Mechoso B, Martínez S, Pagano S, Bellini S, Costabel M, Quadrelli R. Clinical, cytogenetic, and molecular characterization of a girl with some clinical features of Down syndrome resulting from a pure partial trisomy 21q22.11-qter due to a de novo intrachromosomal duplication. Genet Test Mol Biomarkers 2010; 14:57-65. [PMID: 20143912 DOI: 10.1089/gtmb.2009.0067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report a girl with a de novo pure partial trisomy 21 with some clinical features of Down syndrome. The girl patient presented a flat broad face, brachycephaly, and a flat nasal bridge. She also had upwardly slanted palpebral fissures, epicanthal folds, blepharitis, brushfield spots, and strabismus. Her mouth was wide with downturned corners, prominent lower lip, narrow and furrowed tongue, and short palate. G-banded chromosomal analysis of metaphases in cells from both skin and blood showed a 46,XX karyotype with additional chromosomal material on the distal short arm of one chromosome 21. Parental chromosomes were normal. Molecular analyses with the short-tandem-repeat (STR) marker D21S2039 (interferon-alpha/beta receptor [IFNAR]) (21q22.1) showed a triallelic pattern. Subtelomeric fluorescent in situ hybridization (FISH) analyses, LSI 13 (retinoblastoma 1 [RB1])/LSI 21(21q22.13-q22.2), and whole chromosome painting probes specific for chromosome 21 showed trisomy for the segment 21q22.13-21q22.2 due to a de novo intrachromosomal duplication. A 500K SNP microarray analysis was then performed and revealed a 13-Mb duplication of 21q22.11-qter. This duplicated material had been translocated onto the end of the "p" arm of one of the chromosome 21s. The karyotype was provisionally defined as 46,XX,add(21)(p12).ish der (21)t(21;21)(p12;q22.11)(WCP21q+,PCP21q++,D215259/D21S341/D21S342++)dn. At the age of 4 years and 10 months, a comprehensive psychological examination was performed and the diagnostic criteria for mental retardation were not fulfilled. In comparison with previously published cases of pure partial trisomy 21, this is a rare finding. Additional studies of such rare patients should aid in the study of the pathogenesis of Down syndrome.
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Affiliation(s)
- Alicia Vaglio
- Institute of Medical Genetics, Hospital Italiano, Montevideo, Uruguay.
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11
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Ronan A, Fagan K, Christie L, Conroy J, Nowak NJ, Turner G. Familial 4.3 Mb duplication of 21q22 sheds new light on the Down syndrome critical region. BMJ Case Rep 2009; 2009:bcr05.2009.1914. [PMID: 21686961 DOI: 10.1136/bcr.05.2009.1914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A 4.3 Mb duplication of chromosome 21 bands q22.13-q22.2 was diagnosed by interphase fluorescent in situ hybridisation (FISH) in a 31 week gestational age baby with cystic hygroma and hydrops; the duplication was later found in the mother and in her 8-year-old daughter. All had the facial gestalt of Down syndrome (DS). This is the smallest accurately defined duplication of chromosome 21 reported with a DS phenotype. The duplication encompasses the gene DYRK1 but not DSCR1 or DSCAM. Previous karyotype analysis and telomere screening of the mother, and karyotype analysis and metaphase FISH of a chorionic villus sample, had all failed to reveal the duplication. The findings in this family add to the identification and delineation of a "critical region" for the DS phenotype on chromosome 21.
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Affiliation(s)
- Anne Ronan
- Hunter Genetics Unit, Waratah, New South Wales, Australia
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12
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Demirtas H. AgNOR status in Down's syndrome infants and a plausible phenotype formation hypothesis. Micron 2009; 40:511-8. [PMID: 19339189 DOI: 10.1016/j.micron.2009.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Revised: 02/25/2009] [Accepted: 02/25/2009] [Indexed: 10/21/2022]
Abstract
Down's syndrome (DS) or trisomy 21 is the most frequent genetic birth defect associated with mental retardation. Although DS has been known for more than a 100 years and its chromosomal basis recognized for half a century (1959), the underlying patho-mechanisms for the phenotype formation remain elusive and cannot be fully explained by simple gene dosage effect. The general consensus is that the extra chromosome 21 genes perturb the global metabolism of the body cells. Our experiments show that the most prominent metabolic perturbation occurs during ribosome biogenesis in the cells of DS babies/infants. In humans, ribosomal RNA (rRNA) gene families or nucleolar organizer regions (NORs) are localized at the secondary constriction (on the satellite stalks) of five pairs of acrocentric chromosomes (13, 14, 15, 21 and 22) and their activities are evaluated specifically either in metaphase or interphase through a procedure known as AgNOR or silver staining. Our successive AgNOR studies, supported by RNA and nuclear protein measurement, show that cells from DS infants produce more ribosomes than expected, accounting for the extra set of active rRNA gene family (1/6-1/11) situated on the extra chromosome 21. Thus, the presence of an extra chromosome 21 stimulates a global increase in ribosome biogenesis in cooperation with other NOR-bearing chromosomes, causing unnecessary rRNA and ribosomal proteins synthesis compared to controls. Following the description of NORs, AgNOR, AgNOR-proteins, AgNOR measurement and our experimental results, we propose that the extra RNA and protein synthesis can cause a fundamental handicap to DS infants, contributing to the formation of DS phenotypes, due to the wasted energy in producing unnecessary macromolecules, including energy (GTP)-dependent transport of the excessive ribosomes from the nucleus to the cytoplasm.
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Affiliation(s)
- Halil Demirtas
- Erciyes University, Medical Faculty, Medical Biology Department 38039 Kayseri, Turkey.
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13
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Abstract
Congenital heart defects occur in nearly 1% of human live births and many are lethal if not surgically repaired. In addition, the genetic contribution to congenital or acquired cardiovascular diseases that are silent at birth, but progress to cause significant disease in later life is being increasingly appreciated. Heart development and structure are highly conserved between mouse and human. The discoveries that are being made in this model system are highly relevant to understanding the pathogenesis of human heart defects whether they occus in isolation, or in the context of a syndrome. Many of the genes required for cardiovascular development were discovered fortuitously when early lethality or structural defects were observed in mouse mutants generated for other purposes, and relevant genes continue to be defined in this manner. Candidate genes for this process are being identified by their roles other species, or by their expression in pertinent tissues in mice. In this review, I will briefly summarize heart development as currently understood in the mouse, and then discuss how complementary studies in mouse and human have identified genes and pathways that are critical for normal cardiovascular development, and for maintaining the structure and function of this organ system throughout life.
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Affiliation(s)
- Anne Moon
- School of Medicine, University of Utah, Salt Lake City, UT 84112, USA
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14
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Ronan A, Fagan K, Christie L, Conroy J, Nowak NJ, Turner G. Familial 4.3 Mb duplication of 21q22 sheds new light on the Down syndrome critical region. J Med Genet 2007; 44:448-51. [PMID: 17237124 PMCID: PMC2598003 DOI: 10.1136/jmg.2006.047373] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/05/2007] [Accepted: 01/08/2007] [Indexed: 11/04/2022]
Abstract
A 4.3 Mb duplication of chromosome 21 bands q22.13-q22.2 was diagnosed by interphase fluorescent in-situ hybridisation (FISH) in a 31-week gestational age baby with cystic hygroma and hydrops; the duplication was later found in the mother and in her 8-year-old daughter by the same method and confirmed by array comparative genomic hybridisation (aCGH). All had the facial gestalt of Down syndrome (DS). This is the smallest accurately defined duplication of chromosome 21 reported with a DS phenotype. The duplication encompasses the gene DYRK1 but not DSCR1 or DSCAM, all of which have previously been implicated in the causation of DS. Previous karyotype analysis and telomere screening of the mother, and karyotype analysis and metaphase FISH of a chorionic villus sample, had all failed to reveal the duplication. The findings in this family add to the identification and delineation of a "critical region" for the DS phenotype on chromosome 21. Cryptic chromosomal abnormalities can be missed on a routine karyotype for investigation of abnormal prenatal ultrasound findings, lending support to the use of aCGH analysis in this setting.
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15
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Van Vooren S, Thienpont B, Menten B, Speleman F, De Moor B, Vermeesch J, Moreau Y. Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations. Nucleic Acids Res 2007; 35:2533-43. [PMID: 17403693 PMCID: PMC1885641 DOI: 10.1093/nar/gkm054] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g. 4p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at http://www.esat.kuleuven.be/abandapart/.
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Affiliation(s)
- Steven Van Vooren
- Department of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium.
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16
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Xing L, Salas M, Lin CS, Zigman W, Silverman W, Subramaniyam S, Murty VV, Tycko B. Faithful tissue-specific expression of the human chromosome 21-linked COL6A1 gene in BAC-transgenic mice. Mamm Genome 2007; 18:113-22. [PMID: 17334655 DOI: 10.1007/s00335-006-0082-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 11/27/2006] [Indexed: 11/30/2022]
Abstract
We created transgenic mice with a bacterial artificial chromosome (BAC) containing the human COL6A1 gene. In high-copy and low-copy transgenic lines, we found correct temporal and spatial expression of COL6A1 mRNA, paralleling the expression of the murine Col6a1 gene in a panel of nine adult and four fetal organs. The only exception was the fetal lung, in which the transgene was expressed poorly compared with the endogenous gene. Expression of COL6A1 mRNA from the transgene was copy number-dependent, and the increased gene dosage correlated with increased production of collagen VI alpha 1 in skin and heart, as indicated by Western blotting and immunohistochemistry. COL6A1 maps to Chromosome 21 and this gene has been a candidate for contributing to cardiac defects and skin abnormalities in Down syndrome. The low-copy and high-copy COL6A1 transgenics were born and survived in normal Mendelian proportions, without cardiac malformations or altered skin histology. These data indicate that the major promoter and enhancer sequences regulating COL6A1 expression are present in this 167-kb BAC clone. The lack of a strong cardiac or skin phenotype in the COL6A1 BAC-transgenic mice suggests that the increased expression of this gene does not, by itself, account for these phenotypes in Down syndrome.
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Affiliation(s)
- Luzhou Xing
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, New York 10032, USA
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Sato D, Kawara H, Shimokawa O, Harada N, Tonoki H, Takahashi N, Imai Y, Kimura H, Matsumoto N, Ariga T, Niikawa N, Yoshiura KI. A girl with Down syndrome and partial trisomy for 21pter-q22.13: A clue to narrow the Down syndrome critical region. Am J Med Genet A 2007; 146A:124-7. [PMID: 18074380 DOI: 10.1002/ajmg.a.31974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daisuke Sato
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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18
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Li CM, Guo M, Salas M, Schupf N, Silverman W, Zigman WB, Husain S, Warburton D, Thaker H, Tycko B. Cell type-specific over-expression of chromosome 21 genes in fibroblasts and fetal hearts with trisomy 21. BMC MEDICAL GENETICS 2006; 7:24. [PMID: 16539728 PMCID: PMC1435874 DOI: 10.1186/1471-2350-7-24] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 03/15/2006] [Indexed: 11/18/2022]
Abstract
Background Down syndrome (DS) is caused by trisomy 21 (+21), but the aberrations in gene expression resulting from this chromosomal aneuploidy are not yet completely understood. Methods We used oligonucleotide microarrays to survey mRNA expression in early- and late-passage control and +21 fibroblasts and mid-gestation fetal hearts. We supplemented this analysis with northern blotting, western blotting, real-time RT-PCR, and immunohistochemistry. Results We found chromosome 21 genes consistently over-represented among the genes over-expressed in the +21 samples. However, these sets of over-expressed genes differed across the three cell/tissue types. The chromosome 21 gene MX1 was strongly over-expressed (mean 16-fold) in senescent +21 fibroblasts, a result verified by northern and western blotting. MX1 is an interferon target gene, and its mRNA was induced by interferons present in +21 fibroblast conditioned medium, suggesting an autocrine loop for its over-expression. By immunohistochemistry the p78MX1 protein was induced in lesional tissue of alopecia areata, an autoimmune disorder associated with DS. We found strong over-expression of the purine biosynthesis gene GART (mean 3-fold) in fetal hearts with +21 and verified this result by northern blotting and real-time RT-PCR. Conclusion Different subsets of chromosome 21 genes are over-expressed in different cell types with +21, and for some genes this over-expression is non-linear (>1.5X). Hyperactive interferon signaling is a candidate pathway for cell senescence and autoimmune disorders in DS, and abnormal purine metabolism should be investigated for a potential role in cardiac defects.
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Affiliation(s)
- Chi-Ming Li
- Institute for Cancer Genetics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Meirong Guo
- Institute for Cancer Genetics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Martha Salas
- Institute for Cancer Genetics, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | - Wayne Silverman
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | - Warren B Zigman
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, New York, NY, USA
| | - Sameera Husain
- Department of Pathology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Dorothy Warburton
- Department of Pathology, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Harshwardhan Thaker
- Department of Pathology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Department of Pathology, Columbia University College of Physicians and Surgeons, New York, NY, USA
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