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Larsen LA, Hitz MP. Human Genetics of Atrial Septal Defect. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:467-480. [PMID: 38884726 DOI: 10.1007/978-3-031-44087-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Although atrial septal defects (ASD) can be subdivided based on their anatomical location, an essential aspect of human genetics and genetic counseling is distinguishing between isolated and familiar cases without extracardiac features and syndromic cases with the co-occurrence of extracardiac abnormalities, such as developmental delay. Isolated or familial cases tend to show genetic alterations in genes related to important cardiac transcription factors and genes encoding for sarcomeric proteins. By contrast, the spectrum of genes with genetic alterations observed in syndromic cases is diverse. Currently, it points to different pathways and gene networks relevant to the dysregulation of cardiomyogenesis and ASD pathogenesis. Therefore, this chapter reflects the current knowledge and highlights stable associations observed in human genetics studies. It gives an overview of the different types of genetic alterations in these subtypes, including common associations based on genome-wide association studies (GWAS), and it highlights the most frequently observed syndromes associated with ASD pathogenesis.
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Affiliation(s)
- Lars A Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marc-Phillip Hitz
- Institute of Medical Genetics, University Medicine Oldenburg, Oldenburg, Germany.
- Department for Paediatric Cardiology, University Hospital Kiel, Kiel, Germany.
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Rashkin SR, Cleves M, Shaw GM, Nembhard WN, Nestoridi E, Jenkins MM, Romitti PA, Lou XY, Browne ML, Mitchell LE, Olshan AF, Lomangino K, Bhattacharyya S, Witte JS, Hobbs CA. A genome-wide association study of obstructive heart defects among participants in the National Birth Defects Prevention Study. Am J Med Genet A 2022; 188:2303-2314. [PMID: 35451555 PMCID: PMC9283270 DOI: 10.1002/ajmg.a.62759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 01/19/2023]
Abstract
Obstructive heart defects (OHDs) share common structural lesions in arteries and cardiac valves, accounting for ~25% of all congenital heart defects. OHDs are highly heritable, resulting from interplay among maternal exposures, genetic susceptibilities, and epigenetic phenomena. A genome-wide association study was conducted in National Birth Defects Prevention Study participants (Ndiscovery = 3978; Nreplication = 2507), investigating the genetic architecture of OHDs using transmission/disequilibrium tests (TDT) in complete case-parental trios (Ndiscovery_TDT = 440; Nreplication_TDT = 275) and case-control analyses separately in infants (Ndiscovery_CCI = 1635; Nreplication_CCI = 990) and mothers (case status defined by infant; Ndiscovery_CCM = 1703; Nreplication_CCM = 1078). In the TDT analysis, the SLC44A2 single nucleotide polymorphism (SNP) rs2360743 was significantly associated with OHD (pdiscovery = 4.08 × 10-9 ; preplication = 2.44 × 10-4 ). A CAPN11 SNP (rs55877192) was suggestively associated with OHD (pdiscovery = 1.61 × 10-7 ; preplication = 0.0016). Two other SNPs were suggestively associated (p < 1 × 10-6 ) with OHD in only the discovery sample. In the case-control analyses, no SNPs were genome-wide significant, and, even with relaxed thresholds ( × discovery < 1 × 10-5 and preplication < 0.05), only one SNP (rs188255766) in the infant analysis was associated with OHDs (pdiscovery = 1.42 × 10-6 ; preplication = 0.04). Additional SNPs with pdiscovery < 1 × 10-5 were in loci supporting previous findings but did not replicate. Overall, there was modest evidence of an association between rs2360743 and rs55877192 and OHD and some evidence validating previously published findings.
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Affiliation(s)
- Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Mario Cleves
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Health Informatics Institute, Tampa, Florida, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Wendy N Nembhard
- Department of Epidemiology and Arkansas Center for Birth Defects and Prevention, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Eirini Nestoridi
- Massachusetts Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul A Romitti
- Department of Epidemiology, University of Iowa, Iowa City, Iowa, USA
| | - Xiang-Yang Lou
- Department of Biostatistics, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marilyn L Browne
- Birth Defects Research Section, New York State Department of Health, Albany, New York, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, New York, USA
| | - Laura E Mitchell
- Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, USA
| | - Andrew F Olshan
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Sudeepa Bhattacharyya
- Bioinformatics and Data Science at University of Arkansas, Little Rock, Arkansas, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
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Liu Y, Williams SG, Jones HR, Keavney BD, Choy MK. A novel RNA-mediated mechanism causing down-regulation of insulating promoter interactions in human embryonic stem cells. Sci Rep 2021; 11:23233. [PMID: 34853328 PMCID: PMC8636647 DOI: 10.1038/s41598-021-02373-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/15/2021] [Indexed: 12/01/2022] Open
Abstract
The genome-wide promoter interactome is primarily maintained and regulated by architectural proteins such as CTCF and cohesin. However, some studies suggest a role for non-coding RNAs (ncRNAs) in this process. We aimed to characterise the regulatory role of RNA-mediated promoter interactions in the control of gene expression. We integrated genome-wide datasets of RNA-chromatin and promoter-genome interactions in human embryonic stem cells (hESCs) to identify putative RNA-mediated promoter interactions. We discovered that CTCF sites were enriched in RNA-PIRs (promoter interacting regions co-localising with RNA-chromatin interaction sites) and genes interacting with RNA-PIRs containing CTCF sites showed higher expression levels. One of the long noncoding RNAs (lncRNAs) expressed in hESCs, Syntaxin 18-Antisense 1 (STX18-AS1), appeared to be involved in an insulating promoter interaction with the neighbouring gene, MSX1. By knocking down STX18-AS1, the MSX1 promoter-PIR interaction was intensified and the target gene (MSX1) expression was down-regulated. Conversely, reduced MSX1 promoter-PIR interactions, resulting from CRISPR-Cas9 deletion of the PIR, increased the expression of MSX1. We conclude that STX18-AS1 RNA antagonised local CTCF-mediated insulating promoter interactions to augment gene expression. Such down-regulation of the insulating promoter interactions by this novel mechanism may explain the higher expression of genes interacting with RNA-PIRs linked to CTCF sites.
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Affiliation(s)
- Yingjuan Liu
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Simon G Williams
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Hayden R Jones
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
- Manchester Heart Institute, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Mun-Kit Choy
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK.
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Association between the 4p16 genomic locus and different types of congenital heart disease: results from adult survivors in the UK Biobank. Sci Rep 2019; 9:16515. [PMID: 31712678 PMCID: PMC6848143 DOI: 10.1038/s41598-019-52969-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/18/2019] [Indexed: 11/17/2022] Open
Abstract
Congenital heart disease is the most common birth defect in newborns and the leading cause of death in infancy, affecting nearly 1% of live births. A locus in chromosome 4p16, adjacent to MSX1 and STX18, has been associated with atrial septal defects (ASD) in multiple European and Chinese cohorts. Here, genotyping data from the UK Biobank was used to test for associations between this locus and congenital heart disease in adult survivors of left ventricular outflow tract obstruction (n = 164) and ASD (n = 223), with a control sample of 332,788 individuals, and a meta-analysis of the new and existing ASD data was performed. The results show an association between the previously reported markers at 4p16 and risk for either ASD or left ventricular outflow tract obstruction, with effect sizes similar to the published data (OR between 1.27–1.45; all p < 0.05). Differences in allele frequencies remained constant through the studied age range (40–70 years), indicating that the variants themselves do not drive lethal genetic defects. Meta-analysis shows an OR of 1.35 (95% CI: 1.25–1.46; p < 10−4) for the association with ASD. The findings show that the genetic associations with ASD can be generalized to adult survivors of both ASD and left ventricular lesions. Although the 4p16 associations are statistically compelling, the mentioned alleles confer only a small risk for disease and their frequencies in this adult sample are the same as in children, likely limiting their clinical significance. Further epidemiological and functional studies may elicit factors triggering disease in interaction with the risk alleles.
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