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McKean DM, Zhang Q, Narayan P, Morton SU, Strohmenger V, Tang VT, McAllister S, Sharma A, Quiat D, Reichart D, DeLaughter DM, Wakimoto H, Gorham JM, Brown K, McDonough B, Willcox JA, Jang MY, DePalma SR, Ward T, Kim R, Cleveland JD, Seidman J, Seidman CE. Increased endothelial sclerostin caused by elevated DSCAM mediates multiple trisomy 21 phenotypes. J Clin Invest 2024; 134:e167811. [PMID: 38828726 PMCID: PMC11142749 DOI: 10.1172/jci167811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/11/2024] [Indexed: 06/05/2024] Open
Abstract
Trisomy 21 (T21), a recurrent aneuploidy occurring in 1:800 births, predisposes to congenital heart disease (CHD) and multiple extracardiac phenotypes. Despite a definitive genetic etiology, the mechanisms by which T21 perturbs development and homeostasis remain poorly understood. We compared the transcriptome of CHD tissues from 49 patients with T21 and 226 with euploid CHD (eCHD). We resolved cell lineages that misexpressed T21 transcripts by cardiac single-nucleus RNA sequencing and RNA in situ hybridization. Compared with eCHD samples, T21 samples had increased chr21 gene expression; 11-fold-greater levels (P = 1.2 × 10-8) of SOST (chr17), encoding the Wnt inhibitor sclerostin; and 1.4-fold-higher levels (P = 8.7 × 10-8) of the SOST transcriptional activator ZNF467 (chr7). Euploid and T21 cardiac endothelial cells coexpressed SOST and ZNF467; however, T21 endothelial cells expressed 6.9-fold more SOST than euploid endothelial cells (P = 2.7 × 10-27). Wnt pathway genes were downregulated in T21 endothelial cells. Expression of DSCAM, residing within the chr21 CHD critical region, correlated with SOST (P = 1.9 × 10-5) and ZNF467 (P = 2.9 × 10-4). Deletion of DSCAM from T21 endothelial cells derived from human induced pluripotent stem cells diminished sclerostin secretion. As Wnt signaling is critical for atrioventricular canal formation, bone health, and pulmonary vascular homeostasis, we concluded that T21-mediated increased sclerostin levels would inappropriately inhibit Wnt activities and promote Down syndrome phenotypes. These findings imply therapeutic potential for anti-sclerostin antibodies in T21.
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Affiliation(s)
- David M. McKean
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Priyanka Narayan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Sarah U. Morton
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Walter Brendle Centre of Experimental Medicine, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Vi T. Tang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sophie McAllister
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ananya Sharma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Barbara McDonough
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jon A. Willcox
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Min Young Jang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven R. DePalma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Richard Kim
- Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - John D. Cleveland
- Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - J.G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, USA
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Ohanele C, Peoples JN, Karlstaedt A, Geiger JT, Gayle AD, Ghazal N, Sohani F, Brown ME, Davis ME, Porter GA, Faundez V, Kwong JQ. Mitochondrial citrate carrier SLC25A1 is a dosage-dependent regulator of metabolic reprogramming and morphogenesis in the developing heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.22.541833. [PMID: 37292906 PMCID: PMC10245819 DOI: 10.1101/2023.05.22.541833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The developing mammalian heart undergoes an important metabolic shift from glycolysis toward mitochondrial oxidation, such that oxidative phosphorylation defects may present with cardiac abnormalities. Here, we describe a new mechanistic link between mitochondria and cardiac morphogenesis, uncovered by studying mice with systemic loss of the mitochondrial citrate carrier SLC25A1. Slc25a1 null embryos displayed impaired growth, cardiac malformations, and aberrant mitochondrial function. Importantly, Slc25a1 heterozygous embryos, which are overtly indistinguishable from wild type, exhibited an increased frequency of these defects, suggesting Slc25a1 haploinsuffiency and dose-dependent effects. Supporting clinical relevance, we found a near-significant association between ultrarare human pathogenic SLC25A1 variants and pediatric congenital heart disease. Mechanistically, SLC25A1 may link mitochondria to transcriptional regulation of metabolism through epigenetic control of gene expression to promote metabolic remodeling in the developing heart. Collectively, this work positions SLC25A1 as a novel mitochondrial regulator of ventricular morphogenesis and cardiac metabolic maturation and suggests a role in congenital heart disease.
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Wang D, Wen X, Xu LL, Chen QX, Yan TX, Xiao HT, Xu XW. Nf1 in heart development: a potential causative gene for congenital heart disease: a narrative review. Physiol Genomics 2023; 55:415-426. [PMID: 37519249 DOI: 10.1152/physiolgenomics.00024.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/26/2023] [Accepted: 07/08/2023] [Indexed: 08/01/2023] Open
Abstract
Congenital heart disease is the most frequent congenital disorder, affecting a significant number of live births. Gaining insights into its genetic etiology could lead to a deeper understanding of this condition. Although the Nf1 gene has been identified as a potential causative gene, its role in congenital heart disease has not been thoroughly clarified. We searched and summarized evidence from cohort-based and experimental studies on the issue of Nf1 and heart development in congenital heart diseases from various databases. Available evidence demonstrates a correlation between Nf1 and congenital heart diseases, mainly pulmonary valvar stenosis. The mechanism underlying this correlation may involve dysregulation of epithelial-mesenchymal transition (EMT). The Nf1 gene affects the EMT process via multiple pathways, including directly regulating the expression of EMT-related transcription factors and indirectly regulating the EMT process by regulating the MAPK pathway. This narrative review provides a comprehensive account of the Nf1 involvement in heart development and congenital cardiovascular diseases in terms of epidemiology and potential mechanisms. RAS signaling may contribute to congenital heart disease independently or in cooperation with other signaling pathways. Efficient management of both NF1 and cardiovascular disease patients would benefit from further research into these issues.
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Affiliation(s)
- Dun Wang
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue Wen
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Li-Li Xu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Qing-Xing Chen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Tian-Xing Yan
- Central Laboratory, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Hai-Tao Xiao
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue-Wen Xu
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
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Ganapathi M, Matsuoka LS, March M, Li D, Brokamp E, Benito-Sanz S, White SM, Lachlan K, Ahimaz P, Sewda A, Bastarache L, Thomas-Wilson A, Stoler JM, Bramswig NC, Baptista J, Stals K, Demurger F, Cogne B, Isidor B, Bedeschi MF, Peron A, Amiel J, Zackai E, Schacht JP, Iglesias AD, Morton J, Schmetz A, Seidel V, Lucia S, Baskin SM, Thiffault I, Cogan JD, Gordon CT, Chung WK, Bowdin S, Bhoj E. Heterozygous rare variants in NR2F2 cause a recognizable multiple congenital anomaly syndrome with developmental delays. Eur J Hum Genet 2023; 31:1117-1124. [PMID: 37500725 PMCID: PMC10545729 DOI: 10.1038/s41431-023-01434-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Nuclear receptor subfamily 2 group F member 2 (NR2F2 or COUP-TF2) encodes a transcription factor which is expressed at high levels during mammalian development. Rare heterozygous Mendelian variants in NR2F2 were initially identified in individuals with congenital heart disease (CHD), then subsequently in cohorts of congenital diaphragmatic hernia (CDH) and 46,XX ovotesticular disorders/differences of sexual development (DSD); however, the phenotypic spectrum associated with pathogenic variants in NR2F2 remains poorly characterized. Currently, less than 40 individuals with heterozygous pathogenic variants in NR2F2 have been reported. Here, we review the clinical and molecular details of 17 previously unreported individuals with rare heterozygous NR2F2 variants, the majority of which were de novo. Clinical features were variable, including intrauterine growth restriction (IUGR), CHD, CDH, genital anomalies, DSD, developmental delays, hypotonia, feeding difficulties, failure to thrive, congenital and acquired microcephaly, dysmorphic facial features, renal failure, hearing loss, strabismus, asplenia, and vascular malformations, thus expanding the phenotypic spectrum associated with NR2F2 variants. The variants seen were predicted loss of function, including a nonsense variant inherited from a mildly affected mosaic mother, missense and a large deletion including the NR2F2 gene. Our study presents evidence for rare, heterozygous NR2F2 variants causing a highly variable syndrome of congenital anomalies, commonly associated with heart defects, developmental delays/intellectual disability, dysmorphic features, feeding difficulties, hypotonia, and genital anomalies. Based on the new and previous cases, we provide clinical recommendations for evaluating individuals diagnosed with an NR2F2-associated disorder.
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Affiliation(s)
- Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Michael March
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dong Li
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elly Brokamp
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara Benito-Sanz
- CIBERER, ISCIII. Institute of Medical and Molecular Genetics (INGEMM), Disorder of Sex Development Multidisciplinary Unit, Hospital Universitario La Paz, Madrid, Spain
| | - Susan M White
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton, UK
- Department of Human Genetics and Genomic Medicine, Southampton University, Southampton, UK
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Anshuman Sewda
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amanda Thomas-Wilson
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joan M Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nuria C Bramswig
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
- Peninsula Medical School, Faculty of Health, University of Plymouth, PL4 8AA, Plymouth, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | | | - Benjamin Cogne
- Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000, Nantes, France
| | - Bertrand Isidor
- Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000, Nantes, France
| | | | - Angela Peron
- Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Università degli Studi di Milano, Milan, Italy
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Jeanne Amiel
- INSERM UMR1163, Institut Imagine, Université Paris-Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Elaine Zackai
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John P Schacht
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandro D Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Ariane Schmetz
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Verónica Seidel
- Clinical Genetics, Department of Pediatrics, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Stephanie Lucia
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephanie M Baskin
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah Bowdin
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals NHS, Foundation Trust, Cambridge, UK
| | - Elizabeth Bhoj
- Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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5
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Hays T, Hernan R, Disco M, Griffin EL, Goldshtrom N, Vargas D, Krishnamurthy G, Bomback M, Rehman AU, Wilson AT, Guha S, Phadke S, Okur V, Robinson D, Felice V, Abhyankar A, Jobanputra V, Chung WK. Implementation of Rapid Genome Sequencing for Critically Ill Infants With Complex Congenital Heart Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:415-420. [PMID: 37417234 DOI: 10.1161/circgen.122.004050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/16/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Rapid genome sequencing (rGS) has been shown to improve care of critically ill infants. Congenital heart disease (CHD) is a leading cause of infant mortality and is often caused by genetic disorders, yet the utility of rGS has not been prospectively studied in this population. METHODS We conducted a prospective evaluation of rGS to improve the care of infants with complex CHD in our cardiac neonatal intensive care unit. RESULTS In a cohort of 48 infants with complex CHD, rGS diagnosed 14 genetic disorders in 13 (27%) individuals and led to changes in clinical management in 8 (62%) cases with diagnostic results. These included 2 cases in whom genetic diagnoses helped avert intensive, futile interventions before cardiac neonatal intensive care unit discharge, and 3 cases in whom eye disease was diagnosed and treated in early childhood. CONCLUSIONS Our study provides the first prospective evaluation of rGS for infants with complex CHD to our knowledge. We found that rGS diagnosed genetic disorders in 27% of cases and led to changes in management in 62% of cases with diagnostic results. Our model of care depended on coordination between neonatologists, cardiologists, surgeons, geneticists, and genetic counselors. These findings highlight the important role of rGS in CHD and demonstrate the need for expanded study of how to implement this resource to a broader population of infants with CHD.
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Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Rebecca Hernan
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Michele Disco
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Emily L Griffin
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Nimrod Goldshtrom
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Diana Vargas
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Ganga Krishnamurthy
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Miles Bomback
- Feinberg School of Medicine, Northwestern University, Chicago, IL (M.B.)
| | - Atteeq U Rehman
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Amanda T Wilson
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Saurav Guha
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Shruti Phadke
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Volkan Okur
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Dino Robinson
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Vanessa Felice
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Avinash Abhyankar
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Vaidehi Jobanputra
- Department of Pathology & Cell Biology (V.J.), Columbia University Irving Medical Center, New York, NY
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Wendy K Chung
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
- Department of Medicine (W.K.C.), Columbia University Irving Medical Center, New York, NY
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Harvey DC, Verma R, Sedaghat B, Hjelm BE, Morton SU, Seidman JG, Kumar SR. Mutations in genes related to myocyte contraction and ventricular septum development in non-syndromic tetralogy of Fallot. Front Cardiovasc Med 2023; 10:1249605. [PMID: 37840956 PMCID: PMC10569225 DOI: 10.3389/fcvm.2023.1249605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/08/2023] [Indexed: 10/17/2023] Open
Abstract
Objective Eighty percent of patients with a diagnosis of tetralogy of Fallot (TOF) do not have a known genetic etiology or syndrome. We sought to identify key molecular pathways and biological processes that are enriched in non-syndromic TOF, the most common form of cyanotic congenital heart disease, rather than single driver genes to elucidate the pathogenesis of this disease. Methods We undertook exome sequencing of 362 probands with non-syndromic TOF and their parents within the Pediatric Cardiac Genomics Consortium (PCGC). We identified rare (minor allele frequency <1 × 10-4), de novo variants to ascertain pathways and processes affected in this population to better understand TOF pathogenesis. Pathways and biological processes enriched in the PCGC TOF cohort were compared to 317 controls without heart defects (and their parents) from the Simons Foundation Autism Research Initiative (SFARI). Results A total of 120 variants in 117 genes were identified as most likely to be deleterious, with CHD7, CLUH, UNC13C, and WASHC5 identified in two probands each. Gene ontology analyses of these variants using multiple bioinformatic tools demonstrated significant enrichment in processes including cell cycle progression, chromatin remodeling, myocyte contraction and calcium transport, and development of the ventricular septum and ventricle. There was also a significant enrichment of target genes of SOX9, which is critical in second heart field development and whose loss results in membranous ventricular septal defects related to disruption of the proximal outlet septum. None of these processes was significantly enriched in the SFARI control cohort. Conclusion Innate molecular defects in cardiac progenitor cells and genes related to their viability and contractile function appear central to non-syndromic TOF pathogenesis. Future research utilizing our results is likely to have significant implications in stratification of TOF patients and delivery of personalized clinical care.
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Affiliation(s)
- Drayton C. Harvey
- Departments of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Riya Verma
- Departments of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Brandon Sedaghat
- Department of Medicine, Rosalind Franklin University School of Medicine and Science, Chicago, IL, United States
| | - Brooke E. Hjelm
- Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Sarah U. Morton
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
| | - Jon G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - S. Ram Kumar
- Departments of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Surgery, University of Nebraska Medical Center, Omaha, NE, United States
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Yao S, Yang T, Kong X, Dang Y, Chen P, Lyu M. The Influence of Maternal Condition on Fetal Cardiac Function during the Second Trimester. Diagnostics (Basel) 2023; 13:2755. [PMID: 37685293 PMCID: PMC10486346 DOI: 10.3390/diagnostics13172755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVE Maternal health has a direct, profound and lasting effect on the formation and development of the fetal cardiovascular system. The aim of this research was to find whether maternal age, BMI hypertension (GH) or gestational diabetic mellitus (GDM) would affect fetal cardiac function in the second trimester. METHOD 329 mothers who had a fetal echocardiogram examination at the International Peace Maternity & Child Health Hospital of China Welfare Institute, Shanghai, China, from 1 January 2020 to 30 April 2020 were enrolled at the gestational age of 21 to 26 weeks (mean 22.78 ± 1.13 weeks). Single-factor analysis and multi-factor line regression analysis were used to find the contribution values of each factor to fetal cardiac function. RESULTS at the second trimester, maternal age had a minor influence on the fetal left ventricle diastolic function. Higher maternal BMI could cause a decrease in the fetal diastolic function of both the left and right ventricle and the systolic function of the left ventricle. Maternal hypertension and gestational diabetic mellitus had a profound influence on both the left and right fetal heart ventricles of both systolic and diastolic function. CONCLUSION maternal condition will have a profound influence on fetal cardiac function as early as the second trimester.
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Affiliation(s)
- Shifa Yao
- Ultrasound Department, The International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Y.); (T.Y.); (X.K.); (Y.D.); (P.C.)
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
| | - Tian Yang
- Ultrasound Department, The International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Y.); (T.Y.); (X.K.); (Y.D.); (P.C.)
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
| | - Xiaoxiao Kong
- Ultrasound Department, The International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Y.); (T.Y.); (X.K.); (Y.D.); (P.C.)
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
| | - Yuanyuan Dang
- Ultrasound Department, The International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Y.); (T.Y.); (X.K.); (Y.D.); (P.C.)
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
| | - Ping Chen
- Ultrasound Department, The International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Y.); (T.Y.); (X.K.); (Y.D.); (P.C.)
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
| | - Mingli Lyu
- Ultrasound Department, The International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (S.Y.); (T.Y.); (X.K.); (Y.D.); (P.C.)
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
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8
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Zhong G, Choi YA, Shen Y. VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Commun Biol 2023; 6:774. [PMID: 37491581 PMCID: PMC10368729 DOI: 10.1038/s42003-023-05155-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
Rare or de novo variants have substantial contribution to human diseases, but the statistical power to identify risk genes by rare variants is generally low due to rarity of genotype data. Previous studies have shown that risk genes usually have high expression in relevant cell types, although for many conditions the identity of these cell types are largely unknown. Recent efforts in single cell atlas in human and model organisms produced large amount of gene expression data. Here we present VBASS, a Bayesian method that integrates single-cell expression and de novo variant (DNV) data to improve power of disease risk gene discovery. VBASS models disease risk prior as a function of expression profiles, approximated by deep neural networks. It learns the weights of neural networks and parameters of Gamma-Poisson likelihood models of DNV counts jointly from expression and genetics data. On simulated data, VBASS shows proper error rate control and better power than state-of-the-art methods. We applied VBASS to published datasets and identified more candidate risk genes with supports from literature or data from independent cohorts. VBASS can be generalized to integrate other types of functional genomics data in statistical genetics analysis.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Yoolim A Choi
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
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9
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Cashman TJ, Trivedi CM. Chromatin Compaction in Noncompaction Cardiomyopathy. Circ Res 2023; 133:68-70. [PMID: 37347831 PMCID: PMC10289807 DOI: 10.1161/circresaha.123.323015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Affiliation(s)
- Timothy J Cashman
- Division of Cardiovascular Medicine, UMass Chan Medical School, Worcester, MA 01605 USA
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01605 USA
| | - Chinmay M. Trivedi
- Division of Cardiovascular Medicine, UMass Chan Medical School, Worcester, MA 01605 USA
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01605 USA
- Department of Molecular, Cell, and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605 USA
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10
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Shi W, Scialdone AP, Emerson JI, Mei L, Wasson LK, Davies HA, Seidman CE, Seidman JG, Cook JG, Conlon FL. Missense Mutation in Human CHD4 Causes Ventricular Noncompaction by Repressing ADAMTS1. Circ Res 2023; 133:48-67. [PMID: 37254794 PMCID: PMC10284140 DOI: 10.1161/circresaha.122.322223] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Left ventricular noncompaction (LVNC) is a prevalent cardiomyopathy associated with excessive trabeculation and thin compact myocardium. Patients with LVNC are vulnerable to cardiac dysfunction and at high risk of sudden death. Although sporadic and inherited mutations in cardiac genes are implicated in LVNC, understanding of the mechanisms responsible for human LVNC is limited. METHODS We screened the complete exome sequence database of the Pediatrics Cardiac Genomics Consortium and identified a cohort with a de novo CHD4 (chromodomain helicase DNA-binding protein 4) proband, CHD4M202I, with congenital heart defects. We engineered a humanized mouse model of CHD4M202I (mouse CHD4M195I). Histological analysis, immunohistochemistry, flow cytometry, transmission electron microscopy, and echocardiography were used to analyze cardiac anatomy and function. Ex vivo culture, immunopurification coupled with mass spectrometry, transcriptional profiling, and chromatin immunoprecipitation were performed to deduce the mechanism of CHD4M195I-mediated ventricular wall defects. RESULTS CHD4M195I/M195I mice developed biventricular hypertrabeculation and noncompaction and died at birth. Proliferation of cardiomyocytes was significantly increased in CHD4M195I hearts, and the excessive trabeculation was associated with accumulation of ECM (extracellular matrix) proteins and a reduction of ADAMTS1 (ADAM metallopeptidase with thrombospondin type 1 motif 1), an ECM protease. We rescued the hyperproliferation and hypertrabeculation defects in CHD4M195I hearts by administration of ADAMTS1. Mechanistically, the CHD4M195I protein showed augmented affinity to endocardial BRG1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4). This enhanced affinity resulted in the failure of derepression of Adamts1 transcription such that ADAMTS1-mediated trabeculation termination was impaired. CONCLUSIONS Our study reveals how a single mutation in the chromatin remodeler CHD4, in mice or humans, modulates ventricular chamber maturation and that cardiac defects associated with the missense mutation CHD4M195I can be attenuated by the administration of ADAMTS1.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Angel P. Scialdone
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - James I. Emerson
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Liu Mei
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
| | - Haley A. Davies
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Jonathan G. Seidman
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
| | - Jeanette G. Cook
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Frank L. Conlon
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
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11
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Zhu W, Lo CW. Insights into the genetic architecture of congenital heart disease from animal modeling. Zool Res 2023; 44:577-590. [PMID: 37147909 PMCID: PMC10236297 DOI: 10.24272/j.issn.2095-8137.2022.463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
Congenital heart disease (CHD) is observed in up to 1% of live births and is one of the leading causes of mortality from birth defects. While hundreds of genes have been implicated in the genetic etiology of CHD, their role in CHD pathogenesis is still poorly understood. This is largely a reflection of the sporadic nature of CHD, as well as its variable expressivity and incomplete penetrance. We reviewed the monogenic causes and evidence for oligogenic etiology of CHD, as well as the role of de novo mutations, common variants, and genetic modifiers. For further mechanistic insight, we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts. Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis, thereby facilitating early intervention to improve outcomes for patients with CHD.
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Affiliation(s)
- Wenjuan Zhu
- Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology-Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201 USA. E-mail:
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12
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Griffin EL, Nees SN, Morton SU, Wynn J, Patel N, Jobanputra V, Robinson S, Kochav SM, Tao A, Andrews C, Cross N, Geva J, Lanzilotta K, Ritter A, Taillie E, Thompson A, Meyer C, Akers R, King EC, Cnota JF, Kim RW, Porter GA, Brueckner M, Seidman CE, Shen Y, Gelb BD, Goldmuntz E, Newburger JW, Roberts AE, Chung WK. Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:e003791. [PMID: 36803080 PMCID: PMC10121846 DOI: 10.1161/circgen.122.003791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/28/2022] [Indexed: 02/23/2023]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common major congenital anomaly and causes significant morbidity and mortality. Epidemiologic evidence supports a role of genetics in the development of CHD. Genetic diagnoses can inform prognosis and clinical management. However, genetic testing is not standardized among individuals with CHD. We sought to develop a list of validated CHD genes using established methods and to evaluate the process of returning genetic results to research participants in a large genomic study. METHODS Two-hundred ninety-five candidate CHD genes were evaluated using a ClinGen framework. Sequence and copy number variants involving genes in the CHD gene list were analyzed in Pediatric Cardiac Genomics Consortium participants. Pathogenic/likely pathogenic results were confirmed on a new sample in a clinical laboratory improvement amendments-certified laboratory and disclosed to eligible participants. Adult probands and parents of probands who received results were asked to complete a post-disclosure survey. RESULTS A total of 99 genes had a strong or definitive clinical validity classification. Diagnostic yields for copy number variants and exome sequencing were 1.8% and 3.8%, respectively. Thirty-one probands completed clinical laboratory improvement amendments-confirmation and received results. Participants who completed postdisclosure surveys reported high personal utility and no decision regret after receiving genetic results. CONCLUSIONS The application of ClinGen criteria to CHD candidate genes yielded a list that can be used to interpret clinical genetic testing for CHD. Applying this gene list to one of the largest research cohorts of CHD participants provides a lower bound for the yield of genetic testing in CHD.
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Affiliation(s)
- Emily L. Griffin
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Shannon N. Nees
- Nemours Cardiac Center, Nemours Children’s Hospital, Delaware. Wilmington, DE
| | - Sarah U. Morton
- Division of Newborn Medicine, Dept of Medicine, Boston Children’s Hospital
- Dept of Pediatrics, Harvard Medical School, Boston, MA
| | - Julia Wynn
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Nihir Patel
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Dept of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Scott Robinson
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Stephanie M. Kochav
- Division of Cardiology, Dept of Medicine, Columbia University Vagelos College of Physicians & Surgeons, New York, NY
| | - Alice Tao
- Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Carli Andrews
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Nancy Cross
- Division of Pediatric Cardiology, Yale School of Medicine, New Haven, CT
| | - Judith Geva
- Dept of Cardiology, Boston Children’s Hospital
| | - Kristen Lanzilotta
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Alyssa Ritter
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
- Division of Human Genetics, Dept of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Eileen Taillie
- Dept of Pediatrics, Golisano Children’s Hospital, University of Rochester Medical Center, Rochester, NY
| | - Alexandra Thompson
- Division of Cardiothoracic Surgery, Children’s Hospital of Los Angeles, Los Angeles, CA
| | | | - Rachel Akers
- Division of Biostatistics & Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Eileen C. King
- Division of Biostatistics & Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - James F Cnota
- The Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Richard W. Kim
- Pediatric Cardiac Surgery, Children's Hospital of Los Angeles, Los Angeles, CA
| | - George A. Porter
- Dept of Pediatrics, University of Rochester Medical Center, The School of Medicine & Dentistry, Rochester, NY
| | - Martina Brueckner
- Dept of Genetics & Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Christine E. Seidman
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA
- Dept of Genetics, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Yufeng Shen
- Depts of Systems Biology & Biomedical Informatics, Columbia University, New York, NY
| | - Bruce D. Gelb
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Depts of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Jane W. Newburger
- Dept of Pediatrics, Harvard Medical School, Boston, MA
- Dept of Cardiology, Boston Children’s Hospital
| | - Amy E. Roberts
- Dept of Cardiology, Boston Children’s Hospital
- Division of Genetics, Dept of Pediatrics, Boston Children’s Hospital
| | - Wendy K. Chung
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Dept of Medicine, Columbia University Irving Medical Center, New York, NY
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13
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Wang H, Xiao F, Qian Y, Wu B, Dong X, Lu Y, Cheng G, Wang L, Yan K, Yang L, Chen L, Kang W, Li L, Pan X, Wei Q, Zhuang D, Chen D, Yin Z, Yang L, Ni Q, Liu R, Li G, Zhang P, Li X, Peng X, Wang Y, Chen H, Ma X, Liu F, Cao Y, Huang G, Zhou W. Genetic architecture in neonatal intensive care unit patients with congenital heart defects: a retrospective study from the China Neonatal Genomes Project. J Med Genet 2023; 60:247-253. [PMID: 35595280 DOI: 10.1136/jmedgenet-2021-108354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/02/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Congenital heart defects (CHDs) are the most common type of birth defects. The genetic aetiology of CHD is complex and incompletely understood. The overall distribution of genetic causes in patients with CHD from neonatal intensive care units (NICUs) needs to be studied. METHODS CHD cases were extracted from the China Neonatal Genomes Project (2016-2021). Next-generation sequencing results and medical records were retrospectively evaluated to note the frequency of genetic diagnosis and the respective patient outcomes. RESULTS In total, 1795 patients were included. The human phenotype ontology term of atrial septal defect, patent ductus arteriosus and ventricular septal defect account for a large portion of the CHD subtype. Co-occurring extracardiac anomalies were observed in 35.1% of patients. 269 of the cases received genetic diagnoses that could explain the phenotype of CHDs, including 172 copy number variations and 97 pathogenic variants. The detection rate of trio-whole-exome sequencing was higher than clinical exome sequencing (21.8% vs 14.5%, p<0.05). Further follow-up analysis showed the genetic diagnostic rate was higher in the deceased group than in the surviving group (29.0% vs 11.9%, p<0.05). CONCLUSION This is the largest cohort study to explore the genetic spectrum of patients with CHD in the NICU in China. Our findings may benefit future work on improving genetic screening and counselling for NICU patients with CHD.
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Affiliation(s)
- Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Feifan Xiao
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Kai Yan
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Liping Chen
- Department of Neonatology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Wenqing Kang
- Department of Neonatology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Long Li
- Department of Neonatology, The People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Xinnian Pan
- Department of Neonatology, Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Qiufen Wei
- Department of Neonatology, Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Deyi Zhuang
- Department of Pediatrics, Xiamen Children's Hospital, Xiamen, Fujian, China
| | - Dongmei Chen
- Department of Neonatal Intensive Care Unit, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, China
| | - Zhaoqing Yin
- Department of Neonatology, The People's Hospital of Dehong, Dehong, Yunnan, China
| | - Ling Yang
- Department of Neonatology, Hainan Women and Children's Medical Center, Haikou, Hainan, China
| | - Qi Ni
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xu Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaomin Peng
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yao Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaojing Ma
- Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Fang Liu
- Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoying Huang
- Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China .,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China .,Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
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14
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Mohammadi T, Mohammadi B. Neuropsychological features in children and adults with congenital heart disease: an exploratory data analysis. PSYCHOL HEALTH MED 2023; 28:693-706. [PMID: 36377086 DOI: 10.1080/13548506.2022.2147558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We aimed to recognize clinically meaningful patterns among patients with congenital heart disease to support clinical decision-making and better classification in practice. This research was a secondary analysis of data from the Congenital Heart Disease Genetic Network Study conducted from December 2010 to November 2014 in the United States. The analytic dataset included 6002 patients ≥1 year of age with non-syndromic congenital heart disease. For each patient, features included demographic, clinical, maternal and paternal characteristics. We clustered patients to identify subgroups that shared similarities in their clinical features. The performance of the clustering algorithm was evaluated with a random forest. Next, we used the apriori algorithm to generate clinical rules from patients' characteristics. The clustering algorithm identified two discernible groups of patients. The two classes of patients were different in maternal diabetes and in neuropsychological indicators [Accuracy (95% CI) = 97.1% (96.2, 97.8), area under the ROC curve = 96.8%]. Our rule extraction suggested the presence of clinical pictures with high lift values among patients with maternal diabetes or with seizure, depression, attention-deficit hyperactivity disorder, anxiety, developmental delay, learning disability and speech problem. Beyond the age of 1 year, maternal diabetes and neuropsychological characteristics identify two clusters of patients with congenital heart disease. These characteristics have the potential of being incorporated into the current systems for the classification of congenital heart disease.
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Affiliation(s)
- Tanya Mohammadi
- College of Science, School of Mathematics, Statistics, and Computer Science, The University of Tehran, Tehran, Iran
| | - Babak Mohammadi
- Independent Researcher, Aja University of Medical Sciences Tehran, Iran
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15
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Martin-Trujillo A, Garg P, Patel N, Jadhav B, Sharp AJ. Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation. Genome Res 2023; 33:184-196. [PMID: 36577521 PMCID: PMC10069470 DOI: 10.1101/gr.277057.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Short tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. Although the effect of STR variation on gene expression has been extensively assessed, their impact on epigenetics has been poorly studied and limited to specific genomic regions. Here, we investigated the hypothesis that some STRs act as independent regulators of local DNA methylation in the human genome and modify risk of common human traits. To address these questions, we first analyzed two independent data sets comprising PCR-free whole-genome sequencing (WGS) and genome-wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using HipSTR, we identified 11,870 STRs that associated with DNA methylation levels (mSTRs) of 11,774 CpGs (Bonferroni P < 0.001) in our discovery cohort, with 90% successfully replicating in our second cohort. Subsequently, through fine-mapping using CAVIAR we defined 585 of these mSTRs as the likely causal variants underlying the observed associations (fm-mSTRs) and linked a fraction of these to previously reported genome-wide association study signals, providing insights into the mechanisms underlying complex human traits. Furthermore, by integrating gene expression data, we observed that 12.5% of the tested fm-mSTRs also modulate expression levels of nearby genes, reinforcing their regulatory potential. Overall, our findings expand the catalog of functional sequence variants that affect genome regulation, highlighting the importance of incorporating STRs in future genetic association analysis and epigenetics data for the interpretation of trait-associated variants.
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Affiliation(s)
- Alejandro Martin-Trujillo
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Paras Garg
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Nihir Patel
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Bharati Jadhav
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, New York 10029, USA
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16
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Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan A, Vadgama N, Balsubramani A, Wu JC, Engreitz JM, Farh K, Karakikes I, Wang KC, Quertermous T, Greenleaf WJ, Kundaje A. Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease. Cell 2022; 185:4937-4953.e23. [PMID: 36563664 PMCID: PMC10122433 DOI: 10.1016/j.cell.2022.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 09/13/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
To define the multi-cellular epigenomic and transcriptional landscape of cardiac cellular development, we generated single-cell chromatin accessibility maps of human fetal heart tissues. We identified eight major differentiation trajectories involving primary cardiac cell types, each associated with dynamic transcription factor (TF) activity signatures. We contrasted regulatory landscapes of iPSC-derived cardiac cell types and their in vivo counterparts, which enabled optimization of in vitro differentiation of epicardial cells. Further, we interpreted sequence based deep learning models of cell-type-resolved chromatin accessibility profiles to decipher underlying TF motif lexicons. De novo mutations predicted to affect chromatin accessibility in arterial endothelium were enriched in congenital heart disease (CHD) cases vs. controls. In vitro studies in iPSCs validated the functional impact of identified variation on the predicted developmental cell types. This work thus defines the cell-type-resolved cis-regulatory sequence determinants of heart development and identifies disruption of cell type-specific regulatory elements in CHD.
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Affiliation(s)
- Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Laksshman Sundaram
- Department of Computer Science, Stanford University, Stanford, CA, USA; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Mengcheng Shen
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Abhimanyu Banerjee
- Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA; Department of Physics, Stanford University, Stanford, CA, USA
| | - Soumya Kundu
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Mingxia Gu
- Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Avyay Varadarajan
- Department of Computer Science, California Institute of Technology, Pasadena, CA, USA
| | - Nirmal Vadgama
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | | | - Joseph C Wu
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA.
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA.
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA.
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17
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Wang YJ, Zhang X, Lam CK, Guo H, Wang C, Zhang S, Wu JC, Snyder M, Li J. Systems analysis of de novo mutations in congenital heart diseases identified a protein network in the hypoplastic left heart syndrome. Cell Syst 2022; 13:895-910.e4. [PMID: 36167075 PMCID: PMC9671831 DOI: 10.1016/j.cels.2022.09.001] [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: 12/02/2021] [Revised: 05/14/2022] [Accepted: 09/02/2022] [Indexed: 01/26/2023]
Abstract
Despite a strong genetic component, only a few genes have been identified in congenital heart diseases (CHDs). We introduced systems analyses to uncover the hidden organization on biological networks of mutations in CHDs and leveraged network analysis to integrate the protein interactome, patient exomes, and single-cell transcriptomes of the developing heart. We identified a CHD network regulating heart development and observed that a sub-network also regulates fetal brain development, thereby providing mechanistic insights into the clinical comorbidities between CHDs and neurodevelopmental conditions. At a small scale, we experimentally verified uncharacterized cardiac functions of several proteins. At a global scale, our study revealed developmental dynamics of the network and observed its association with the hypoplastic left heart syndrome (HLHS), which was further supported by the dysregulation of the network in HLHS endothelial cells. Overall, our work identified previously uncharacterized CHD factors and provided a generalizable framework applicable to studying many other complex diseases. A record of this paper's Transparent Peer Review process is included in the supplemental information.
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Affiliation(s)
- Yuejun Jessie Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Bakar Computational Health Sciences Institute, the Parker Institute for Cancer Immunotherapy, and the Department of Neurology, School of Medicine, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Xicheng Zhang
- Department of Genetics and the Center for Genomics and Personalized Medicine, School of Medicine, Stanford University, 291 Campus Dr., Stanford, CA 94305, USA
| | - Chi Keung Lam
- Stanford Cardiovascular Institute, School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA; Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Hongchao Guo
- Stanford Cardiovascular Institute, School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA
| | - Cheng Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Bakar Computational Health Sciences Institute, the Parker Institute for Cancer Immunotherapy, and the Department of Neurology, School of Medicine, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Sai Zhang
- Department of Genetics and the Center for Genomics and Personalized Medicine, School of Medicine, Stanford University, 291 Campus Dr., Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA; Department of Radiology, Stanford University School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA
| | - Michael Snyder
- Department of Genetics and the Center for Genomics and Personalized Medicine, School of Medicine, Stanford University, 291 Campus Dr., Stanford, CA 94305, USA; Stanford Cardiovascular Institute, School of Medicine, Stanford University, 265 Campus Dr., Stanford, CA 94305, USA.
| | - Jingjing Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Bakar Computational Health Sciences Institute, the Parker Institute for Cancer Immunotherapy, and the Department of Neurology, School of Medicine, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA.
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18
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Choudhury TZ, Garg V. Molecular genetic mechanisms of congenital heart disease. Curr Opin Genet Dev 2022; 75:101949. [PMID: 35816939 PMCID: PMC9673038 DOI: 10.1016/j.gde.2022.101949] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/28/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
Congenital heart disease (CHD) affects ~1% of all live births, but a definitive etiology is identified in only ~50%. The causes include chromosomal aneuploidies and copy-number variations, pathogenic variation in single genes, and exposure to environmental factors. High-throughput sequencing of large CHD patient cohorts and continued expansion of the complex molecular regulation of cardiac morphogenesis has uncovered numerous disease-causing genes, but the previously held monogenic model for CHD etiology does not sufficiently explain the heterogeneity and incomplete penetrance of CHD phenotypes. Here, we provide a summary of well-known genetic contributors to CHD and discuss emerging concepts supporting complex genetic mechanisms that may provide explanations for cases that currently lack a molecular diagnosis.
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Affiliation(s)
- Talita Z Choudhury
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Heart Center, Nationwide Children's Hospital, Columbus, OH, USA.
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Heart Center, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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19
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Gordon DM, Cunningham D, Zender G, Lawrence PJ, Penaloza JS, Lin H, Fitzgerald-Butt SM, Myers K, Duong T, Corsmeier DJ, Gaither JB, Kuck HC, Wijeratne S, Moreland B, Kelly BJ, Garg V, White P, McBride KL. Exome sequencing in multiplex families with left-sided cardiac defects has high yield for disease gene discovery. PLoS Genet 2022; 18:e1010236. [PMID: 35737725 PMCID: PMC9258875 DOI: 10.1371/journal.pgen.1010236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/06/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022] Open
Abstract
Congenital heart disease (CHD) is a common group of birth defects with a strong genetic contribution to their etiology, but historically the diagnostic yield from exome studies of isolated CHD has been low. Pleiotropy, variable expressivity, and the difficulty of accurately phenotyping newborns contribute to this problem. We hypothesized that performing exome sequencing on selected individuals in families with multiple members affected by left-sided CHD, then filtering variants by population frequency, in silico predictive algorithms, and phenotypic annotations from publicly available databases would increase this yield and generate a list of candidate disease-causing variants that would show a high validation rate. In eight of the nineteen families in our study (42%), we established a well-known gene/phenotype link for a candidate variant or performed confirmation of a candidate variant’s effect on protein function, including variants in genes not previously described or firmly established as disease genes in the body of CHD literature: BMP10, CASZ1, ROCK1 and SMYD1. Two plausible variants in different genes were found to segregate in the same family in two instances suggesting oligogenic inheritance. These results highlight the need for functional validation and demonstrate that in the era of next-generation sequencing, multiplex families with isolated CHD can still bring high yield to the discovery of novel disease genes. Congenital heart disease is a common group of birth defects that are a leading cause of death in children under one year of age. There is strong evidence that genetics plays a role in causing congenital heart disease. While studies using individual cases have identified causative genes for those with a heart defect when accompanied by other birth defects or intellectual disabilities, for individuals who have only a heart defect without other problems, a genetic cause can be found in fewer than 10%. In this study, we enrolled families where there was more than one individual with a heart defect. This allowed us to take advantage of inheritance by searching for potential disease-causing genetic variants in common among all affected individuals in the family. Among 19 families studied, we were able to find a plausible disease-causing variant in eight of them and identified new genes that may cause or contribute to the presence of a heart defect. Two families had potential disease-causing variants in two different genes. We designed assays to test if the variants led to altered function of the protein coded by the gene, demonstrating a functional consequence that support the gene and variant as contributing to the heart defect. These findings show that studying families may be more effective than using individuals to find causes of heart defects. In addition, this family-based method suggests that changes in more than one gene may be required for a heart defect to occur.
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Affiliation(s)
- David M. Gordon
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - David Cunningham
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Gloria Zender
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Patrick J. Lawrence
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jacqueline S. Penaloza
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Hui Lin
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Sara M. Fitzgerald-Butt
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Katherine Myers
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Tiffany Duong
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Donald J. Corsmeier
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jeffrey B. Gaither
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Harkness C. Kuck
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Saranga Wijeratne
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Blythe Moreland
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Benjamin J. Kelly
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | | | - Vidu Garg
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (PW); (KLM)
| | - Peter White
- Computational Genomics Group, The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (PW); (KLM)
| | - Kim L. McBride
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (VG); (PW); (KLM)
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20
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Morton SU, Pereira AC, Quiat D, Richter F, Kitaygorodsky A, Hagen J, Bernstein D, Brueckner M, Goldmuntz E, Kim RW, Lifton RP, Porter GA, Tristani-Firouzi M, Chung WK, Roberts A, Gelb BD, Shen Y, Newburger JW, Seidman JG, Seidman CE. Genome-Wide De Novo Variants in Congenital Heart Disease Are Not Associated With Maternal Diabetes or Obesity. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003500. [PMID: 35130025 PMCID: PMC9295870 DOI: 10.1161/circgen.121.003500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common anomaly at birth, with a prevalence of ≈1%. While infants born to mothers with diabetes or obesity have a 2- to 3-fold increased incidence of CHD, the cause of the increase is unknown. Damaging de novo variants (DNV) in coding regions are more common among patients with CHD, but genome-wide rates of coding and noncoding DNVs associated with these prenatal exposures have not been studied in patients with CHD. METHODS DNV frequencies were determined for 1812 patients with CHD who had whole-genome sequencing and prenatal history data available from the Pediatric Cardiac Genomics Consortium's CHD GENES study (Genetic Network). The frequency of DNVs was compared between subgroups using t test or linear model. RESULTS Among 1812 patients with CHD, the number of DNVs per patient was higher with maternal diabetes (76.5 versus 72.1, t test P=3.03×10-11), but the difference was no longer significant after including parental ages in a linear model (paternal and maternal correction P=0.42). No interaction was observed between diabetes risk and parental age (paternal and maternal interaction P=0.80 and 0.68, respectively). No difference was seen in DNV count per patient based on maternal obesity (72.0 versus 72.2 for maternal body mass index <25 versus maternal body mass index >30, t test P=0.86). CONCLUSIONS After accounting for parental age, the offspring of diabetic or obese mothers have no increase in DNVs compared with other children with CHD. These results emphasize the role for other mechanisms in the cause of CHD associated with these prenatal exposures. REGISTRATION URL: https://clinicaltrials.gov; NCT01196182.
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Affiliation(s)
- Sarah U. Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA USA,Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | | | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, MA USA,Department of Cardiology, Boston Children’s Hospital, Boston, MA USA
| | - Felix Richter
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Alexander Kitaygorodsky
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Jacob Hagen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Daniel Bernstein
- Department of Pediatrics (Cardiology), Stanford University, Stanford, CA USA
| | - Martina Brueckner
- Departments of Genetics and Pediatrics; Yale University School of Medicine, New Haven, CT USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | | | - Richard P. Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY USA
| | - George A. Porter
- Department of Pediatrics, University of Rochester Medical Center, The School of Medicine and Dentistry, Rochester, NY USA
| | | | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY USA
| | - Amy Roberts
- Department of Pediatrics, Harvard Medical School, Boston, MA USA,Department of Cardiology, Boston Children’s Hospital, Boston, MA USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY USA
| | - Jane W. Newburger
- Department of Pediatrics, Harvard Medical School, Boston, MA USA,Department of Cardiology, Boston Children’s Hospital, Boston, MA USA
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA USA,Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA USA,Howard Hughes Medical Institute, Chevy Chase, MD USA
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21
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Ecovoiu AA, Ratiu AC, Micheu MM, Chifiriuc MC. Inter-Species Rescue of Mutant Phenotype—The Standard for Genetic Analysis of Human Genetic Disorders in Drosophila melanogaster Model. Int J Mol Sci 2022; 23:ijms23052613. [PMID: 35269756 PMCID: PMC8909942 DOI: 10.3390/ijms23052613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
Drosophila melanogaster (the fruit fly) is arguably a superstar of genetics, an astonishing versatile experimental model which fueled no less than six Nobel prizes in medicine. Nowadays, an evolving research endeavor is to simulate and investigate human genetic diseases in the powerful D. melanogaster platform. Such a translational experimental strategy is expected to allow scientists not only to understand the molecular mechanisms of the respective disorders but also to alleviate or even cure them. In this regard, functional gene orthology should be initially confirmed in vivo by transferring human or vertebrate orthologous transgenes in specific mutant backgrounds of D. melanogaster. If such a transgene rescues, at least partially, the mutant phenotype, then it qualifies as a strong candidate for modeling the respective genetic disorder in the fruit fly. Herein, we review various examples of inter-species rescue of relevant mutant phenotypes of the fruit fly and discuss how these results recommend several human genes as candidates to study and validate genetic variants associated with human diseases. We also consider that a wider implementation of this evolutionist exploratory approach as a standard for the medicine of genetic disorders would allow this particular field of human health to advance at a faster pace.
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Affiliation(s)
- Alexandru Al. Ecovoiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
| | - Attila Cristian Ratiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania;
- Correspondence: ; Tel.: +40-722250366
| | - Miruna Mihaela Micheu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, 014461 Bucharest, Romania;
| | - Mariana Carmen Chifiriuc
- The Research Institute of the University of Bucharest and Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
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22
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Škorić-Milosavljević D, Tadros R, Bosada FM, Tessadori F, van Weerd JH, Woudstra OI, Tjong FV, Lahrouchi N, Bajolle F, Cordell HJ, Agopian A, Blue GM, Barge-Schaapveld DQ, Gewillig M, Preuss C, Lodder EM, Barnett P, Ilgun A, Beekman L, van Duijvenboden K, Bokenkamp R, Müller-Nurasyid M, Vliegen HW, Konings TC, van Melle JP, van Dijk AP, van Kimmenade RR, Roos-Hesselink JW, Sieswerda GT, Meijboom F, Abdul-Khaliq H, Berger F, Dittrich S, Hitz MP, Moosmann J, Riede FT, Schubert S, Galan P, Lathrop M, Munter HM, Al-Chalabi A, Shaw CE, Shaw PJ, Morrison KE, Veldink JH, van den Berg LH, Evans S, Nobrega MA, Aneas I, Radivojkov-Blagojević M, Meitinger T, Oechslin E, Mondal T, Bergin L, Smythe JF, Altamirano-Diaz L, Lougheed J, Bouma BJ, Chaix MA, Kline J, Bassett AS, Andelfinger G, van der Palen RL, Bouvagnet P, Clur SAB, Breckpot J, Kerstjens-Frederikse WS, Winlaw DS, Bauer UM, Mital S, Goldmuntz E, Keavney B, Bonnet D, Mulder BJ, Tanck MW, Bakkers J, Christoffels VM, Boogerd CJ, Postma AV, Bezzina CR. Common Genetic Variants Contribute to Risk of Transposition of the Great Arteries. Circ Res 2022; 130:166-180. [PMID: 34886679 PMCID: PMC8768504 DOI: 10.1161/circresaha.120.317107] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
Abstract
RATIONALE Dextro-transposition of the great arteries (D-TGA) is a severe congenital heart defect which affects approximately 1 in 4,000 live births. While there are several reports of D-TGA patients with rare variants in individual genes, the majority of D-TGA cases remain genetically elusive. Familial recurrence patterns and the observation that most cases with D-TGA are sporadic suggest a polygenic inheritance for the disorder, yet this remains unexplored. OBJECTIVE We sought to study the role of common single nucleotide polymorphisms (SNPs) in risk for D-TGA. METHODS AND RESULTS We conducted a genome-wide association study in an international set of 1,237 patients with D-TGA and identified a genome-wide significant susceptibility locus on chromosome 3p14.3, which was subsequently replicated in an independent case-control set (rs56219800, meta-analysis P=8.6x10-10, OR=0.69 per C allele). SNP-based heritability analysis showed that 25% of variance in susceptibility to D-TGA may be explained by common variants. A genome-wide polygenic risk score derived from the discovery set was significantly associated to D-TGA in the replication set (P=4x10-5). The genome-wide significant locus (3p14.3) co-localizes with a putative regulatory element that interacts with the promoter of WNT5A, which encodes the Wnt Family Member 5A protein known for its role in cardiac development in mice. We show that this element drives reporter gene activity in the developing heart of mice and zebrafish and is bound by the developmental transcription factor TBX20. We further demonstrate that TBX20 attenuates Wnt5a expression levels in the developing mouse heart. CONCLUSIONS This work provides support for a polygenic architecture in D-TGA and identifies a susceptibility locus on chromosome 3p14.3 near WNT5A. Genomic and functional data support a causal role of WNT5A at the locus.
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Affiliation(s)
- Doris Škorić-Milosavljević
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
| | - Rafik Tadros
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada (R.T., M.-A.C.)
| | - Fernanda M. Bosada
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
| | - Jan Hendrik van Weerd
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Odilia I. Woudstra
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Fleur V.Y. Tjong
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Fanny Bajolle
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Germany (F.B., S.S.)
| | - Heather J. Cordell
- Population Health Sciences Institute, Newcastle University, Newcastle, United Kingdom (H.J.C.)
| | - A.J. Agopian
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, TX (A.J.A.)
| | - Gillian M. Blue
- Heart Centre for Children, The Children’s Hospital at Westmead and Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Australia (G.M.B., D.S.W.)
| | | | | | - Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Québec, Canada (C.P., G.A.)
- The Jackson Laboratory, Bar Harbor, ME (C.P.)
| | - Elisabeth M. Lodder
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
| | - Phil Barnett
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Leander Beekman
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Regina Bokenkamp
- Division of Pediatric Cardiology, Department of Pediatrics (R.B., R.L.F.v.d.P.), Leiden University Medical Center, The Netherlands
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany (M.M.-N.)
- IBE, Faculty of Medicine, LMU Munich, Germany (M.M.-N.)
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany (M.M.-N.)
| | - Hubert W. Vliegen
- Department of Cardiology (H.W.V.), Leiden University Medical Center, The Netherlands
| | - Thelma C. Konings
- Department of Cardiology, Amsterdam University Medical Centers, VU Amsterdam, The Netherlands (T.C.K.)
| | - Joost P. van Melle
- Department of Cardiology, University Medical Center Groningen, University of Groningen, The Netherlands (J.P.v.M.)
| | - Arie P.J. van Dijk
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands (A.P.J.v.D., R.R.J.v.K.)
| | - Roland R.J. van Kimmenade
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands (A.P.J.v.D., R.R.J.v.K.)
- Department of Cardiology, Maastricht University Medical Center, The Netherlands (R.R.J.v.K.)
| | - Jolien W. Roos-Hesselink
- Department of Cardiology, Erasmus Medical Center, Erasmus University, Rotterdam, The Netherlands (J.W.R.-H.)
| | - Gertjan T. Sieswerda
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Folkert Meijboom
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Hashim Abdul-Khaliq
- Saarland University Medical Center, Department of Pediatric Cardiology, Homburg, Germany (H.A.-K.)
| | - Felix Berger
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de référence Malformations Cardiaques Congénitales Complexes - M3C, Hôpital Necker Enfants Malades, APHP and Université Paris Descartes, Sorbonne Paris Cité, Paris, France (F.B., D.B.)
- Charité, Universitätsmedizin Berlin, Department for Paediatric Cardiology, Germany (F.B.)
| | - Sven Dittrich
- Department of Pediatric Cardiology, Friedrich-Alexander-University of Erlangen-Nuernberg (FAU), Germany (S.D., J.M.)
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein/Campus Kiel, DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany (M.-P.H.)
- Department of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany (M.-P.H.)
| | - Julia Moosmann
- Department of Pediatric Cardiology, Friedrich-Alexander-University of Erlangen-Nuernberg (FAU), Germany (S.D., J.M.)
| | - Frank-Thomas Riede
- Leipzig Heart Center, Department of Pediatric Cardiology, University of Leipzig, Germany (F.-T.R.)
| | - Stephan Schubert
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Germany (F.B., S.S.)
- Heart and Diabetes Center NRW, Center of Congenital Heart Disease, Ruhr-University of Bochum, Bad Oeynhausen, Germany (S.S.)
| | - Pilar Galan
- Sorbonne Paris Nord (Paris 13) University, Inserm U1153, Inrae U1125, Cnam, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center – University of Paris (CRESS), Bobigny, France (P.G.)
| | - Mark Lathrop
- McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Québec, Canada (M.L., H.M.M.)
| | - Hans M. Munter
- McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Québec, Canada (M.L., H.M.M.)
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King’s College London, United Kingdom (A.A.-C.)
| | - Christopher E. Shaw
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, United Kingdom (C.E.S.)
- Centre for Brain Research, University of Auckland, New Zealand (C.E.S.)
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield and NIHR Sheffield Biomedical Research Centre for Translational Neuroscience, United Kingdom (P.J.S.)
| | - Karen E. Morrison
- Faculty of Medicine Health & Life Sciences, Queens University Belfast, United Kingdom (K.E.M.)
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands (J.H.V., L.H.v.d.B.)
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands (J.H.V., L.H.v.d.B.)
| | - Sylvia Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (S.E.)
| | | | - Ivy Aneas
- Department of Human Genetics, University of Chicago, IL (M.A.N., I.A.)
| | | | - Thomas Meitinger
- Helmholtz Zentrum Munich, Institut of Human Genetics, Neuherberg, Germany (M.R.-B., T.M.)
- Division of Cardiology, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada (T.M.)
| | - Erwin Oechslin
- Peter Munk Cardiac Center, Toronto Congenital Cardiac Centre for Adults and University of Toronto, Canada (E.O.)
| | - Tapas Mondal
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Germany (T.M.)
| | - Lynn Bergin
- Division of Cardiology, Department of Medicine, London Health Sciences Centre, ON, Canada (L.B.)
| | - John F. Smythe
- Division of Cardiology, Department of Pediatrics, Kingston General Hospital, ON, Canada (J.F.S.)
| | | | - Jane Lougheed
- Division of Cardiology, Department of Pediatrics, Children’s Hospital of Eastern Ontario, Ottawa, Canada (J.L.)
| | - Berto J. Bouma
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Marie-A. Chaix
- Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada (R.T., M.-A.C.)
| | - Jennie Kline
- Department of Epidemiology, Mailman School of Public Health, Columbia University, NY (J.K.)
| | - Anne S. Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health (A.S.B.)
- Department of Psychiatry, University of Toronto, Toronto General Hospital, University Health Network, Ontario, Canada (A.S.B.)
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Québec, Canada (C.P., G.A.)
| | - Roel L.F. van der Palen
- Division of Pediatric Cardiology, Department of Pediatrics (R.B., R.L.F.v.d.P.), Leiden University Medical Center, The Netherlands
| | - Patrice Bouvagnet
- CPDPN, Hôpital MFME, CHU Martinique, Fort de France, Martinique, France (P.B.)
| | - Sally-Ann B. Clur
- Department of Pediatric Cardiology, Emma Children’s Hospital Amsterdam University Medical Centers (AMC), The Netherlands (S.-A.B.C.)
- Centre for Congenital Heart Disease Amsterdam-Leiden (CAHAL) (S.-A.B.C.)
| | - Jeroen Breckpot
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
- Center for Human Genetics University Hospitals KU Leuven, Belgium (J.B.)
| | | | - David S. Winlaw
- Heart Centre for Children, The Children’s Hospital at Westmead and Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Australia (G.M.B., D.S.W.)
| | - Ulrike M.M. Bauer
- National Register for Congenital Heart Defects, DZHK (German Centre for Cardiovascular Research), Berlin, Germany (U.M.M.B.)
| | - Seema Mital
- Hospital for Sick Children, University of Toronto, Ontario, Canada (S.M.)
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (E.G.)
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom (B.K.)
| | - Damien Bonnet
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de référence Malformations Cardiaques Congénitales Complexes - M3C, Hôpital Necker Enfants Malades, APHP and Université Paris Descartes, Sorbonne Paris Cité, Paris, France (F.B., D.B.)
| | - Barbara J. Mulder
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Michael W.T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health (APH), Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (M.W.T.T.)
| | - Jeroen Bakkers
- Division of Heart and Lungs, Department of Medical Physiology, University Medical Center Utrecht, the Netherlands (J.B.)
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Cornelis J. Boogerd
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
| | - Alex V. Postma
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Connie R. Bezzina
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
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23
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Zhang T, Yuan H, Zhu H, Ying Y, Ding J, Ding H, Shi X, He Y, Pan H, Zhong Y. Fetal Congenital Heart Disease Caused by Compound Heterozygous Mutations in the DNAH9 Gene: A Case Report. Front Genet 2022; 12:771756. [PMID: 35116053 PMCID: PMC8804278 DOI: 10.3389/fgene.2021.771756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Fetal congenital heart disease (CHD) is the most common congenital defect, with an incidence of 0.6–0.8%, accounting for 30–50% of infant congenital disease deaths. The pathogenesis of CHD is still unclear, so an active and effective prenatal diagnosis is very important for the prevention and control of CHD. Herein, a Chinese CHD patient with rare compound heterozygous mutations in the DNAH9 gene was reported, and the 3D structure and functional changes of DNAH9 protein were predicted.Case presentation: A 23-year-old pregnant woman came to our hospital for prenatal diagnosis at 27 weeks of gestation. Both she and her partner were unaffected. Fetal CHD was detected by ultrasound screening. Copy number variation sequencing (CNV-seq) revealed an 81 kb deletion at chr17p12 (11,486,795–11,568,385), including exons 1–15 of DNAH9 gene, which plays a key role in cardiac development. Then, whole exome sequencing (WES) was used and identified a nonsense mutation (c.10975C>T) in DNAH9, which resulted in the mutation of amino acid 3,659 from glutamine to termination. The 3D mutant protein structures were predicted using SWISS-MODEL and showed structural changes from functional β-sheet and α-helix to termination, respectively.Conclusion: We describe a case of fetal CHD caused by DNAH9 mutations and provide an effective diagnostic technique for identifying intragenic deletions. This diagnostic process can be implicated in prenatal diagnosis of CHD.
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Affiliation(s)
- Tao Zhang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Hua Yuan
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Hongdan Zhu
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yuyi Ying
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Jinlong Ding
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Haigang Ding
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Xiaoliang Shi
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yao He
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Haitao Pan
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
- *Correspondence: Haitao Pan, ; Yongxing Zhong,
| | - Yongxing Zhong
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
- *Correspondence: Haitao Pan, ; Yongxing Zhong,
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24
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Drosophila Heart as a Model for Cardiac Development and Diseases. Cells 2021; 10:cells10113078. [PMID: 34831301 PMCID: PMC8623483 DOI: 10.3390/cells10113078] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 01/26/2023] Open
Abstract
The Drosophila heart, also referred to as the dorsal vessel, pumps the insect blood, the hemolymph. The bilateral heart primordia develop from the most dorsally located mesodermal cells, migrate coordinately, and fuse to form the cardiac tube. Though much simpler, the fruit fly heart displays several developmental and functional similarities to the vertebrate heart and, as we discuss here, represents an attractive model system for dissecting mechanisms of cardiac aging and heart failure and identifying genes causing congenital heart diseases. Fast imaging technologies allow for the characterization of heartbeat parameters in the adult fly and there is growing evidence that cardiac dysfunction in human diseases could be reproduced and analyzed in Drosophila, as discussed here for heart defects associated with the myotonic dystrophy type 1. Overall, the power of genetics and unsuspected conservation of genes and pathways puts Drosophila at the heart of fundamental and applied cardiac research.
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25
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Environmental Alterations during Embryonic Development: Studying the Impact of Stressors on Pluripotent Stem Cell-Derived Cardiomyocytes. Genes (Basel) 2021; 12:genes12101564. [PMID: 34680959 PMCID: PMC8536136 DOI: 10.3390/genes12101564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/16/2022] Open
Abstract
Non-communicable diseases (NCDs) sauch as diabetes, obesity and cardiovascular diseases are rising rapidly in all countries world-wide. Environmental maternal factors (e.g., diet, oxidative stress, drugs and many others), maternal illnesses and other stressors can predispose the newborn to develop diseases during different stages of life. The connection between environmental factors and NCDs was formulated by David Barker and colleagues as the Developmental Origins of Health and Disease (DOHaD) hypothesis. In this review, we describe the DOHaD concept and the effects of several environmental stressors on the health of the progeny, providing both animal and human evidence. We focus on cardiovascular diseases which represent the leading cause of death worldwide. The purpose of this review is to discuss how in vitro studies with pluripotent stem cells (PSCs), such as embryonic and induced pluripotent stem cells (ESC, iPSC), can underpin the research on non-genetic heart conditions. The PSCs could provide a tool to recapitulate aspects of embryonic development “in a dish”, studying the effects of environmental exposure during cardiomyocyte (CM) differentiation and maturation, establishing a link to molecular mechanism and epigenetics.
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26
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Yasuhara J, Garg V. Genetics of congenital heart disease: a narrative review of recent advances and clinical implications. Transl Pediatr 2021; 10:2366-2386. [PMID: 34733677 PMCID: PMC8506053 DOI: 10.21037/tp-21-297] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Congenital heart disease (CHD) is the most common human birth defect and remains a leading cause of mortality in childhood. Although advances in clinical management have improved the survival of children with CHD, adult survivors commonly experience cardiac and non-cardiac comorbidities, which affect quality of life and prognosis. Therefore, the elucidation of genetic etiologies of CHD not only has important clinical implications for genetic counseling of patients and families but may also impact clinical outcomes by identifying at-risk patients. Recent advancements in genetic technologies, including massively parallel sequencing, have allowed for the discovery of new genetic etiologies for CHD. Although variant prioritization and interpretation of pathogenicity remain challenges in the field of CHD genomics, advances in single-cell genomics and functional genomics using cellular and animal models of CHD have the potential to provide novel insights into the underlying mechanisms of CHD and its associated morbidities. In this review, we provide an updated summary of the established genetic contributors to CHD and discuss recent advances in our understanding of the genetic architecture of CHD along with current challenges with the interpretation of genetic variation. Furthermore, we highlight the clinical implications of genetic findings to predict and potentially improve clinical outcomes in patients with CHD.
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Affiliation(s)
- Jun Yasuhara
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
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27
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Helm BM, Landis BJ, Ware SM. Genetic Evaluation of Inpatient Neonatal and Infantile Congenital Heart Defects: New Findings and Review of the Literature. Genes (Basel) 2021; 12:genes12081244. [PMID: 34440418 PMCID: PMC8391303 DOI: 10.3390/genes12081244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 02/05/2023] Open
Abstract
The use of clinical genetics evaluations and testing for infants with congenital heart defects (CHDs) is subject to practice variation. This single-institution cross-sectional study of all inpatient infants with severe CHDs evaluated 440 patients using a cardiovascular genetics service (2014–2019). In total, 376 (85.5%) had chromosome microarray (CMA), of which 55 (14.6%) were diagnostic in syndromic (N = 35) or isolated (N = 20) presentations. Genetic diagnoses were made in all CHD classes. Diagnostic yield was higher in syndromic appearing infants, but geneticists’ dysmorphology exams lacked complete sensitivity and 6.5% of isolated CHD cases had diagnostic CMA. Interestingly, diagnostic results (15.8%) in left ventricular outflow tract obstruction (LVOTO) defects occurred most often in patients with isolated CHD. Geneticists’ evaluations were particularly important for second-tier molecular testing (10.5% test-specific yield), bringing the overall genetic testing yield to 17%. We assess these results in the context of previous studies. Cumulative evidence provides a rationale for comprehensive, standardized genetic evaluation in infants with severe CHDs regardless of lesion or extracardiac anomalies because genetic diagnoses that impact care are easily missed. These findings support routine CMA testing in infants with severe CHDs and underscore the importance of copy-number analysis with newer testing strategies such as exome and genome sequencing.
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Affiliation(s)
- Benjamin M. Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, IN 46202, USA
- Correspondence: ; Tel.: +1-317-944-3966
| | - Benjamin J. Landis
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Stephanie M. Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
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28
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Teekakirikul P, Zhu W, Gabriel GC, Young CB, Williams K, Martin LJ, Hill JC, Richards T, Billaud M, Phillippi JA, Wang J, Wu Y, Tan T, Devine W, Lin JH, Bais AS, Klonowski J, de Bellaing AM, Saini A, Wang MX, Emerel L, Salamacha N, Wyman SK, Lee C, Li HS, Miron A, Zhang J, Xing J, McNamara DM, Fung E, Kirshbom P, Mahle W, Kochilas LK, He Y, Garg V, White P, McBride KL, Benson DW, Gleason TG, Mital S, Lo CW. Common deletion variants causing protocadherin-α deficiency contribute to the complex genetics of BAV and left-sided congenital heart disease. HGG ADVANCES 2021; 2:100037. [PMID: 34888534 PMCID: PMC8653519 DOI: 10.1016/j.xhgg.2021.100037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/21/2021] [Indexed: 11/11/2022] Open
Abstract
Bicuspid aortic valve (BAV) with ~1%-2% prevalence is the most common congenital heart defect (CHD). It frequently results in valve disease and aorta dilation and is a major cause of adult cardiac surgery. BAV is genetically linked to rare left-heart obstructions (left ventricular outflow tract obstructions [LVOTOs]), including hypoplastic left heart syndrome (HLHS) and coarctation of the aorta (CoA). Mouse and human studies indicate LVOTO is genetically heterogeneous with a complex genetic etiology. Homozygous mutation in the Pcdha protocadherin gene cluster in mice can cause BAV, and also HLHS and other LVOTO phenotypes when accompanied by a second mutation. Here we show two common deletion copy number variants (delCNVs) within the PCDHA gene cluster are associated with LVOTO. Analysis of 1,218 white individuals with LVOTO versus 463 disease-free local control individuals yielded odds ratios (ORs) at 1.47 (95% confidence interval [CI], 1.13-1.92; p = 4.2 × 10-3) for LVOTO, 1.47 (95% CI, 1.10-1.97; p = 0.01) for BAV, 6.13 (95% CI, 2.75-13.7; p = 9.7 × 10-6) for CoA, and 1.49 (95% CI, 1.07-2.08; p = 0.019) for HLHS. Increased OR was observed for all LVOTO phenotypes in homozygous or compound heterozygous PCDHA delCNV genotype comparison versus wild type. Analysis of an independent white cohort (381 affected individuals, 1,352 control individuals) replicated the PCDHA delCNV association with LVOTO. Generalizability of these findings is suggested by similar observations in Black and Chinese individuals with LVOTO. Analysis of Pcdha mutant mice showed reduced PCDHA expression at regions of cell-cell contact in aortic smooth muscle and cushion mesenchyme, suggesting potential mechanisms for BAV pathogenesis and aortopathy. Together, these findings indicate common variants causing PCDHA deficiency play a significant role in the genetic etiology of common and rare LVOTO-CHD.
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Affiliation(s)
- Polakit Teekakirikul
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Centre for Cardiovascular Genomics and Medicine, Division of Cardiology, and Division of Medical Sciences, Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenjuan Zhu
- Centre for Cardiovascular Genomics and Medicine, Division of Cardiology, and Division of Medical Sciences, Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong SAR, China
| | - George C. Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cullen B. Young
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kylia Williams
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lisa J. Martin
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, and Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - Jennifer C. Hill
- Department of Cardiothoracic Surgery and Department of Bioengineering, McGowan Institute for Regenerative Medicine, and Center for Vascular Remodeling and Regeneration, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tara Richards
- Department of Cardiothoracic Surgery and Department of Bioengineering, McGowan Institute for Regenerative Medicine, and Center for Vascular Remodeling and Regeneration, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marie Billaud
- Department of Cardiothoracic Surgery and Department of Bioengineering, McGowan Institute for Regenerative Medicine, and Center for Vascular Remodeling and Regeneration, University of Pittsburgh, Pittsburgh, PA, USA
| | - Julie A. Phillippi
- Department of Cardiothoracic Surgery and Department of Bioengineering, McGowan Institute for Regenerative Medicine, and Center for Vascular Remodeling and Regeneration, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yijen Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tuantuan Tan
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - William Devine
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jiuann-huey Lin
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Abha S. Bais
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jonathan Klonowski
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Moreau de Bellaing
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pediatric Cardiology, Necker-Sick Children Hospital and University of Paris Descartes, Paris, France
| | - Ankur Saini
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael X. Wang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Leonid Emerel
- Department of Cardiothoracic Surgery and Department of Bioengineering, McGowan Institute for Regenerative Medicine, and Center for Vascular Remodeling and Regeneration, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathan Salamacha
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Samuel K. Wyman
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carrie Lee
- Centre for Cardiovascular Genomics and Medicine, Division of Cardiology, and Division of Medical Sciences, Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hung Sing Li
- Centre for Cardiovascular Genomics and Medicine, Division of Cardiology, and Division of Medical Sciences, Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anastasia Miron
- Division of Cardiology, Labatt Family Heart Centre, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Jingyu Zhang
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dennis M. McNamara
- Heart and Vascular Institute, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Erik Fung
- Centre for Cardiovascular Genomics and Medicine, Division of Cardiology, and Division of Medical Sciences, Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong SAR, China
- Laboratory for Heart Failure and Circulation Research, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, CARE Programme, Lui Che Woo Institute of Innovative Medicine, and Gerald Choa Cardiac Research Centre, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul Kirshbom
- Sanger Heart & Vascular Institute, Charlotte, NC, USA
| | - William Mahle
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Lazaros K. Kochilas
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Yihua He
- Department of Ultrasound, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Vidu Garg
- Center for Cardiovascular Research, The Heart Center, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Peter White
- The Institute for Genomic Medicine, Center for Cardiovascular Research, Nationwide Children’s Hospital and Department of Pediatrics, Ohio State University College of Medicine, Columbus, OH, USA
| | - Kim L. McBride
- Center for Cardiovascular Research, The Heart Center, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - D. Woodrow Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas G. Gleason
- Division of Cardiac Surgery, Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Seema Mital
- Division of Cardiology, Labatt Family Heart Centre, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Cecilia W. Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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29
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Diab NS, Barish S, Dong W, Zhao S, Allington G, Yu X, Kahle KT, Brueckner M, Jin SC. Molecular Genetics and Complex Inheritance of Congenital Heart Disease. Genes (Basel) 2021; 12:1020. [PMID: 34209044 PMCID: PMC8307500 DOI: 10.3390/genes12071020] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/09/2023] Open
Abstract
Congenital heart disease (CHD) is the most common congenital malformation and the leading cause of mortality therein. Genetic etiologies contribute to an estimated 90% of CHD cases, but so far, a molecular diagnosis remains unsolved in up to 55% of patients. Copy number variations and aneuploidy account for ~23% of cases overall, and high-throughput genomic technologies have revealed additional types of genetic variation in CHD. The first CHD risk genotypes identified through high-throughput sequencing were de novo mutations, many of which occur in chromatin modifying genes. Murine models of cardiogenesis further support the damaging nature of chromatin modifying CHD mutations. Transmitted mutations have also been identified through sequencing of population scale CHD cohorts, and many transmitted mutations are enriched in cilia genes and Notch or VEGF pathway genes. While we have come a long way in identifying the causes of CHD, more work is required to end the diagnostic odyssey for all CHD families. Complex genetic explanations of CHD are emerging but will require increasingly sophisticated analysis strategies applied to very large CHD cohorts before they can come to fruition in providing molecular diagnoses to genetically unsolved patients. In this review, we discuss the genetic architecture of CHD and biological pathways involved in its pathogenesis.
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Affiliation(s)
- Nicholas S. Diab
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Syndi Barish
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Shujuan Zhao
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
| | - Garrett Allington
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Xiaobing Yu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Kristopher T. Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sheng Chih Jin
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Pediatrics, School of Medicine, Washington University, St. Louis, MO 63110, USA
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30
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Garg P, Martin-Trujillo A, Rodriguez OL, Gies SJ, Hadelia E, Jadhav B, Jain M, Paten B, Sharp AJ. Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. Am J Hum Genet 2021; 108:809-824. [PMID: 33794196 DOI: 10.1016/j.ajhg.2021.03.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/11/2021] [Indexed: 12/27/2022] Open
Abstract
Variable number tandem repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, because of their large size and repetitive nature, they remain poorly studied. To investigate the regulatory potential of VNTRs, we used read-depth data from Illumina whole-genome sequencing to perform association analysis between copy number of ∼70,000 VNTRs (motif size ≥ 10 bp) with both gene expression (404 samples in 48 tissues) and DNA methylation (235 samples in peripheral blood), identifying thousands of VNTRs that are associated with local gene expression (eVNTRs) and DNA methylation levels (mVNTRs). Using an independent cohort, we validated 73%-80% of signals observed in the two discovery cohorts, while allelic analysis of VNTR length and CpG methylation in 30 Oxford Nanopore genomes gave additional support for mVNTR loci, thus providing robust evidence to support that these represent genuine associations. Further, conditional analysis indicated that many eVNTRs and mVNTRs act as QTLs independently of other local variation. We also observed strong enrichments of eVNTRs and mVNTRs for regulatory features such as enhancers and promoters. Using the Human Genome Diversity Panel, we define sets of VNTRs that show highly divergent copy numbers among human populations and show that these are enriched for regulatory effects and preferentially associate with genes that have been linked with human phenotypes through GWASs. Our study provides strong evidence supporting functional variation at thousands of VNTRs and defines candidate sets of VNTRs, copy number variation of which potentially plays a role in numerous human phenotypes.
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31
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Kalayinia S, Maleki M, Mahdavi M, Mahdieh N. Whole-Exome Sequencing Reveals a Novel Mutation of FLNA Gene in an Iranian Family with Nonsyndromic Tetralogy of Fallot. Lab Med 2021; 52:614-618. [PMID: 33942857 DOI: 10.1093/labmed/lmab018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE Tetralogy of Fallot (TOF) is one of the most common congenital abnormalities that need early intervention. Here, for the first time, we report a nonsyndromic form of TOF caused by a novel variant in the FLNA gene in 2 siblings of an Iranian family. METHODS The family underwent a complete workup, including karyotyping, sequencing of 6 common genes in congenital heart diseases (GATA4, NKX2-5, ZIC3, FOXH1, NODAL, and GJA1), array comparative genomic hybridization, multiplex ligation-dependent probe amplification, and whole-exome sequencing. Segregation and in silico analysis were also conducted for the identified variant. RESULTS A variant, c.3415C>T, in the FLNA gene was found in both affected brothers in this family; this variant was heterozygous in their mother. Bioinformatics tools predicted the variant as a pathogenic one. CONCLUSION Many allelic disorders have been reported for FLNA mutations. Mutations in this gene may cause a nonsyndromic congenital form of TOF.
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Affiliation(s)
- Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahdavi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Nejat Mahdieh
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.,Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
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32
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Rufaihah AJ, Chen CK, Yap CH, Mattar CNZ. Mending a broken heart: In vitro, in vivo and in silico models of congenital heart disease. Dis Model Mech 2021; 14:14/3/dmm047522. [PMID: 33787508 PMCID: PMC8033415 DOI: 10.1242/dmm.047522] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Birth defects contribute to ∼0.3% of global infant mortality in the first month of life, and congenital heart disease (CHD) is the most common birth defect among newborns worldwide. Despite the significant impact on human health, most treatments available for this heterogenous group of disorders are palliative at best. For this reason, the complex process of cardiogenesis, governed by multiple interlinked and dose-dependent pathways, is well investigated. Tissue, animal and, more recently, computerized models of the developing heart have facilitated important discoveries that are helping us to understand the genetic, epigenetic and mechanobiological contributors to CHD aetiology. In this Review, we discuss the strengths and limitations of different models of normal and abnormal cardiogenesis, ranging from single-cell systems and 3D cardiac organoids, to small and large animals and organ-level computational models. These investigative tools have revealed a diversity of pathogenic mechanisms that contribute to CHD, including genetic pathways, epigenetic regulators and shear wall stresses, paving the way for new strategies for screening and non-surgical treatment of CHD. As we discuss in this Review, one of the most-valuable advances in recent years has been the creation of highly personalized platforms with which to study individual diseases in clinically relevant settings.
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Affiliation(s)
- Abdul Jalil Rufaihah
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228
| | - Ching Kit Chen
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228
| | - Choon Hwai Yap
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat -National University Children's Medical Institute, National University Health System, Singapore 119228.,Department of Bioengineering, Imperial College London, London, UK
| | - Citra N Z Mattar
- Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228 .,Department of Obstetrics and Gynaecology, National University Health System, Singapore 119228
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33
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Lahrouchi N, Postma AV, Salazar CM, De Laughter DM, Tjong F, Piherová L, Bowling FZ, Zimmerman D, Lodder EM, Ta-Shma A, Perles Z, Beekman L, Ilgun A, Gunst Q, Hababa M, Škorić-Milosavljević D, Stránecký V, Tomek V, de Knijff P, de Leeuw R, Robinson JY, Burn SC, Mustafa H, Ambrose M, Moss T, Jacober J, Niyazov DM, Wolf B, Kim KH, Cherny S, Rousounides A, Aristidou-Kallika A, Tanteles G, Ange-Line B, Denommé-Pichon AS, Francannet C, Ortiz D, Haak MC, Ten Harkel AD, Manten GT, Dutman AC, Bouman K, Magliozzi M, Radio FC, Santen GW, Herkert JC, Brown HA, Elpeleg O, van den Hoff MJ, Mulder B, Airola MV, Kmoch S, Barnett JV, Clur SA, Frohman MA, Bezzina CR. Biallelic loss-of-function variants in PLD1 cause congenital right-sided cardiac valve defects and neonatal cardiomyopathy. J Clin Invest 2021; 131:142148. [PMID: 33645542 DOI: 10.1172/jci142148] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/16/2020] [Indexed: 01/12/2023] Open
Abstract
Congenital heart disease is the most common type of birth defect, accounting for one-third of all congenital anomalies. Using whole-exome sequencing of 2718 patients with congenital heart disease and a search in GeneMatcher, we identified 30 patients from 21 unrelated families of different ancestries with biallelic phospholipase D1 (PLD1) variants who presented predominantly with congenital cardiac valve defects. We also associated recessive PLD1 variants with isolated neonatal cardiomyopathy. Furthermore, we established that p.I668F is a founder variant among Ashkenazi Jews (allele frequency of ~2%) and describe the phenotypic spectrum of PLD1-associated congenital heart defects. PLD1 missense variants were overrepresented in regions of the protein critical for catalytic activity, and, correspondingly, we observed a strong reduction in enzymatic activity for most of the mutant proteins in an enzymatic assay. Finally, we demonstrate that PLD1 inhibition decreased endothelial-mesenchymal transition, an established pivotal early step in valvulogenesis. In conclusion, our study provides a more detailed understanding of disease mechanisms and phenotypic expression associated with PLD1 loss of function.
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Affiliation(s)
- Najim Lahrouchi
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Alex V Postma
- Department of Clinical Genetics, and.,Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands
| | - Christian M Salazar
- Department of Pharmacological Sciences and Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York, USA
| | - Daniel M De Laughter
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Fleur Tjong
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Lenka Piherová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Forrest Z Bowling
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Dominic Zimmerman
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Elisabeth M Lodder
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Asaf Ta-Shma
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Zeev Perles
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Leander Beekman
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands
| | - Quinn Gunst
- Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands
| | - Mariam Hababa
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Doris Škorić-Milosavljević
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Viktor Tomek
- Children's Heart Centre, 2nd Faculty of Medicine, Charles University in Prague, Motol University Hospital, Prague, Czech Republic
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Rick de Leeuw
- Department of Human Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Jamille Y Robinson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Hiba Mustafa
- Department of Obstetrics, Gynecology and Women's Health
| | - Matthew Ambrose
- Department of Pediatrics, Division of Pediatric Cardiology, and
| | - Timothy Moss
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jennifer Jacober
- Department of Pediatrics, Ochsner Clinic, Tulane University, University of Queensland, New Orleans, Louisiana, USA
| | - Dmitriy M Niyazov
- Department of Pediatrics, Ochsner Clinic, Tulane University, University of Queensland, New Orleans, Louisiana, USA
| | - Barry Wolf
- Division of Genetics, Birth Defects and Metabolic Disorders, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Katherine H Kim
- Division of Genetics, Birth Defects and Metabolic Disorders, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Sara Cherny
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Division of Cardiology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | | | | | - George Tanteles
- Cyprus School of Molecular Medicine, Nicosia, Cyprus.,Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Bruel Ange-Line
- UMR 1231 INSERM, GAD, Université Bourgogne Franche-Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostique Génomique des Maladies Rares, FHU-TRANSLAD, Centre Hospitalier Universitaire Estaing (CHU), Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR 1231 INSERM, GAD, Université Bourgogne Franche-Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostique Génomique des Maladies Rares, FHU-TRANSLAD, Centre Hospitalier Universitaire Estaing (CHU), Dijon Bourgogne, Dijon, France
| | | | - Damara Ortiz
- Medical Genetics Department, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Arend D.J. Ten Harkel
- Department of Pediatric Cardiology, Leiden University Medical Centre, Leiden, Netherlands
| | | | - Annemiek C Dutman
- Department of Pathology, Isala Women and Children's Hospital, Zwolle, Netherlands
| | - Katelijne Bouman
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Monia Magliozzi
- Genetic and Rare Disease Research Division, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | | | - Gijs We Santen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Johanna C Herkert
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - H Alex Brown
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | | | - Barbara Mulder
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Joey V Barnett
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Sally-Ann Clur
- Department of Pediatric Cardiology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Michael A Frohman
- Department of Pharmacological Sciences and Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York, USA
| | - Connie R Bezzina
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
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Ward T, Tai W, Morton S, Impens F, Van Damme P, Van Haver D, Timmerman E, Venturini G, Zhang K, Jang MY, Willcox JAL, Haghighi A, Gelb BD, Chung WK, Goldmuntz E, Porter GA, Lifton RP, Brueckner M, Yost HJ, Bruneau BG, Gorham J, Kim Y, Pereira A, Homsy J, Benson CC, DePalma SR, Varland S, Chen CS, Arnesen T, Gevaert K, Seidman C, Seidman JG. Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency. Circ Res 2021; 128:1156-1169. [PMID: 33557580 PMCID: PMC8048381 DOI: 10.1161/circresaha.120.316966] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tarsha Ward
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Warren Tai
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sarah Morton
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Newborn Medicine, Boston Children's Hospital (S.M.)
| | - Francis Impens
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Biochemistry and Microbiology (P.V.D.), Ghent University, B-9000 Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium (F.I., D.V.H., E.T., K.G.).,VIB Proteomics Core, B-9000 Ghent, Belgium (F.I., D.V.H., E.T.).,Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Gabriela Venturini
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,University of Sao Paulo (G.V.)
| | - Kehan Zhang
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Min Young Jang
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jon A L Willcox
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Alireza Haghighi
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - Bruce D Gelb
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York (B.D.G.)
| | - Wendy K Chung
- Pediatrics and Medicine, Columbia University Medical Center, New York (W.K.C.)
| | - Elizabeth Goldmuntz
- Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.)
| | | | - Richard P Lifton
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Laboratory of Human Genetics and Genomics, Rockefeller University, New York (R.P.L.)
| | - Martina Brueckner
- Genetics, Yale University School of Medicine, New Haven (R.P.L., M.B.).,Pediatrics, Yale University School of Medicine, New Haven (M.B.)
| | - H Joseph Yost
- Molecular Medicine Program, University of Utah, Salt Lake City (H.J.Y.)
| | | | - Joshua Gorham
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Yuri Kim
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Division of Cardiovascular Medicine, Brigham and Women's Hospital (Y.K.)
| | - Alexandre Pereira
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Jason Homsy
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Craig C Benson
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Steven R DePalma
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
| | - Sylvia Varland
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada (S.V.)
| | - Christopher S Chen
- Biomedical Engineering, Boston University, MA (K.Z., C.S.C.).,The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA (K.Z., C.S.C.)
| | - Thomas Arnesen
- Biomedicine (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Biological Sciences (S.V., T.A.), University of Bergen, N-5020 Bergen, Norway.,Surgery, Haukeland University Hospital, N-5021 Bergen, Norway (T.A.)
| | - Kris Gevaert
- Biomolecular Medicine (F.I., D.V.H., E.T., K.G.), Ghent University, B-9000 Ghent, Belgium
| | - Christine Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School.,Howard Hughes Medical Institute (A.H., C.S.), Harvard Medical School.,Medicine, Brigham and Women's Hospital (A.H., C.S.)
| | - J G Seidman
- Genetics (T.W., W.T., S.M., G.V., M.Y.J., J.A.L.W., A.H., J.G., Y.K., A.P., J.H., C.C.B., S.R.D., C.S., J.G.S.), Harvard Medical School
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Lin H, McBride KL, Garg V, Zhao MT. Decoding Genetics of Congenital Heart Disease Using Patient-Derived Induced Pluripotent Stem Cells (iPSCs). Front Cell Dev Biol 2021; 9:630069. [PMID: 33585486 PMCID: PMC7873857 DOI: 10.3389/fcell.2021.630069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Congenital heart disease (CHD) is the most common cause of infant death associated with birth defects. Recent next-generation genome sequencing has uncovered novel genetic etiologies of CHD, from inherited and de novo variants to non-coding genetic variants. The next phase of understanding the genetic contributors of CHD will be the functional illustration and validation of this genome sequencing data in cellular and animal model systems. Human induced pluripotent stem cells (iPSCs) have opened up new horizons to investigate genetic mechanisms of CHD using clinically relevant and patient-specific cardiac cells such as cardiomyocytes, endothelial/endocardial cells, cardiac fibroblasts and vascular smooth muscle cells. Using cutting-edge CRISPR/Cas9 genome editing tools, a given genetic variant can be corrected in diseased iPSCs and introduced to healthy iPSCs to define the pathogenicity of the variant and molecular basis of CHD. In this review, we discuss the recent progress in genetics of CHD deciphered by large-scale genome sequencing and explore how genome-edited patient iPSCs are poised to decode the genetic etiologies of CHD by coupling with single-cell genomics and organoid technologies.
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Affiliation(s)
- Hui Lin
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Kim L McBride
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Vidu Garg
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
| | - Ming-Tao Zhao
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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Abstract
Congenital heart disease is the most common congenital defect observed in newborns. Within the spectrum of congenital heart disease are left‐sided obstructive lesions (LSOLs), which include hypoplastic left heart syndrome, aortic stenosis, bicuspid aortic valve, coarctation of the aorta, and interrupted aortic arch. These defects can arise in isolation or as a component of a defined syndrome; however, nonsyndromic defects are often observed in multiple family members and associated with high sibling recurrence risk. This clear evidence for a heritable basis has driven a lengthy search for disease‐causing variants that has uncovered both rare and common variants in genes that, when perturbed in cardiac development, can result in LSOLs. Despite advancements in genetic sequencing platforms and broadening use of exome sequencing, the currently accepted LSOL‐associated genes explain only 10% to 20% of patients. Further, the combinatorial effects of common and rare variants as a cause of LSOLs are emerging. In this review, we highlight the genes and variants associated with the different LSOLs and discuss the strengths and weaknesses of the present genetic associations. Furthermore, we discuss the research avenues needed to bridge the gaps in our current understanding of the genetic basis of nonsyndromic congenital heart disease.
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Affiliation(s)
- Lauren E Parker
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC
| | - Andrew P Landstrom
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC.,Department of Cell Biology Duke University School of Medicine Durham NC
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Peng J, Wang Q, Meng Z, Wang J, Zhou Y, Zhou S, Song W, Chen S, Chen AF, Sun K. A loss-of-function mutation p.T256M in NDRG4 is implicated in the pathogenesis of pulmonary atresia with ventricular septal defect (PA/VSD) and tetralogy of Fallot (TOF). FEBS Open Bio 2021; 11:375-385. [PMID: 33211401 PMCID: PMC7876499 DOI: 10.1002/2211-5463.13044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/10/2020] [Accepted: 11/17/2020] [Indexed: 11/10/2022] Open
Abstract
Pulmonary atresia with ventricular septal defect (PA/VSD) is a rare congenital heart disease (CHD) characterized by a lack of luminal continuity and blood flow from either the right ventricle or the pulmonary artery, together with VSDs. The prevalence of PA/VSD is about 0.2% of live births and approximately 2% of CHDs. PA/VSD is similar to tetralogy of Fallot (TOF) in terms of structural and pathological characteristics. The pathogenesis of these two CHDs remains incompletely understood. It was previously reported that N‐myc downstream‐regulated gene (NDRG)4 is required for myocyte proliferation during early cardiac development. In the present study, we enrolled 80 unrelated patients with PA/VSD or TOF and identified a probably damaging variant p.T256M of NDRG4. The p.T256M variant impaired the proliferation ability of human cardiac myocytes (hCM). Furthermore, the p.T256M variant resulted in G1 and G2 arrest of hCM, followed by an increase in p27 and caspase‐9 expression. Our results provide evidence that the p.T256M variant in NDRG4 is a pathogenic variant associated with impaired hCM proliferation and cell‐cycle arrest and likely contributes towards the pathogenesis of PA/VSD and TOF.
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Affiliation(s)
- Jiayu Peng
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qingjie Wang
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhuo Meng
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhou
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuang Zhou
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Song
- Department of Pediatric Cardiology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Alex F Chen
- Institute of Cardiovascular Development and Regeneration, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kun Sun
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Abstract
Diseases that manifest themselves in the pediatric age group frequently have a more diverse spectrum of abnormalities and a greater rarity than diseases that are primarily seen in adults. The complexity and the relatively small populations with specific diseases are factors that have hindered progress in the treatment of pediatric disorders. Personalized medical therapies that are specifically tailored for individuals with unusual or unique problems have great potential to assist in overcoming these factors that have been a bottleneck to pediatric medical success. Personalization of therapies will necessarily be data driven and will require delineation of the proteomic, genomic, epigenomic, and immune characteristics of patients in comparison to the general population. It follows that there is a need to provide researchers with accessible high-quality pediatric tissue collections to facilitate the acquisition of the molecular information needed to support personalized medicine. Because of the unusual nature of many pediatric diseases, sample pools from individual institutions are often too small to adequately power definitive studies. Thus, etiological and translational research in this area are increasingly relying on biobanking networks to provide investigators with adequate numbers of tissue samples. Several pediatric biobanking networks have been formed, which are aimed at increasing the power of research studies and desired pools of high-quality samples. However, despite the concerted efforts, these multicenter networks and collaborations have met with mixed outcomes owing to increasing complexities and heterogeneity in the biobanking arena. While there have been challenges and roadblocks, there also have been some positive outcomes that have had paradigm impacts on diagnosis, study, and treatment of specific diseases. This article highlights the need for establishing pediatric biobanks, how current efforts in pediatric biobanking are influencing the pediatric research landscape, and attempts to identify practical impediments that continue to hamper advancements for the future.
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Affiliation(s)
- Lalita Wadhwa
- Department of Congenital Heart Surgery, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
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39
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Abstract
PURPOSE OF REVIEW This article reviews the current understanding and limitations in knowledge of the effect genetics and genetic diagnoses have on perioperative and postoperative surgical outcomes in patients with congenital heart disease (CHD). RECENT FINDINGS Presence of a known genetic diagnosis seems to effect multiple significant outcome metrics in CHD surgery including length of stay, need for extracorporeal membrane oxygenation, mortality, bleeding, and heart failure. Data regarding the effects of genetics in CHD is complicated by lack of standard genetic assessment resulting in inaccurate risk stratification of patients when analyzing data. Only 30% of variation in CHD surgical outcomes are explained by currently measured variables, with 2.5% being attributed to diagnosed genetic disorders, it is thought a significant amount of the remaining outcome variation is because of unmeasured genetic factors. SUMMARY Genetic diagnoses clearly have a significant effect on surgical outcomes in patients with CHD. Our current understanding is limited by lack of consistent genetic evaluation and assessment as well as evolving knowledge and discovery regarding the genetics of CHD. Standardizing genetic assessment of patients with CHD will allow for the best risk stratification and ultimate understanding of these effects.
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Martin-Trujillo A, Patel N, Richter F, Jadhav B, Garg P, Morton SU, McKean DM, DePalma SR, Goldmuntz E, Gruber D, Kim R, Newburger JW, Porter GA, Giardini A, Bernstein D, Tristani-Firouzi M, Seidman JG, Seidman CE, Chung WK, Gelb BD, Sharp AJ. Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles. PLoS Genet 2020; 16:e1009189. [PMID: 33216750 PMCID: PMC7679001 DOI: 10.1371/journal.pgen.1009189] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/11/2020] [Indexed: 12/20/2022] Open
Abstract
Although DNA methylation is the best characterized epigenetic mark, the mechanism by which it is targeted to specific regions in the genome remains unclear. Recent studies have revealed that local DNA methylation profiles might be dictated by cis-regulatory DNA sequences that mainly operate via DNA-binding factors. Consistent with this finding, we have recently shown that disruption of CTCF-binding sites by rare single nucleotide variants (SNVs) can underlie cis-linked DNA methylation changes in patients with congenital anomalies. These data raise the hypothesis that rare genetic variation at transcription factor binding sites (TFBSs) might contribute to local DNA methylation patterning. In this work, by combining blood genome-wide DNA methylation profiles, whole genome sequencing-derived SNVs from 247 unrelated individuals along with 133 predicted TFBS motifs derived from ENCODE ChIP-Seq data, we observed an association between the disruption of binding sites for multiple TFs by rare SNVs and extreme DNA methylation values at both local and, to a lesser extent, distant CpGs. While the majority of these changes affected only single CpGs, 24% were associated with multiple outlier CpGs within ±1kb of the disrupted TFBS. Interestingly, disruption of functionally constrained sites within TF motifs lead to larger DNA methylation changes at nearby CpG sites. Altogether, these findings suggest that rare SNVs at TFBS negatively influence TF-DNA binding, which can lead to an altered local DNA methylation profile. Furthermore, subsequent integration of DNA methylation and RNA-Seq profiles from cardiac tissues enabled us to observe an association between rare SNV-directed DNA methylation and outlier expression of nearby genes. In conclusion, our findings not only provide insights into the effect of rare genetic variation at TFBS on shaping local DNA methylation and its consequences on genome regulation, but also provide a rationale to incorporate DNA methylation data to interpret the functional role of rare variants. One of the major challenges for human genetics in the post-genomic era is to interpret the functional relevance of genetic variation. Quantitative trait locus (QTL) analyses have associated an important fraction of genetic variants with a wide range of molecular phenotypes including gene expression (eQTL) and DNA methylation (meQTL), providing insights into the mechanisms by which genetic variation can contribute to health and disease. Although QTL mapping represents an excellent approach to identify biologically relevant functional variants, these studies have been mainly focused on common variants and do not include low-frequency and rare variants. Here, we observed that rare regulatory variants, i.e, single nucleotide variants (SNVs) that disrupt transcription factor binding sites (TFBSs), are associated with changes in DNA methylation at both local and, to a lesser extent, broader locations, most likely, by altering the DNA-binding affinity of transcription factors (TFs). Interestingly, we have also shown that this change in DNA methylation can alter expression levels of nearby genes. Overall, these data suggest a role of rare regulatory SNVs in shaping DNA methylation, and suggest that the incorporation of DNA methylation data may help to interpret the functional consequences of human genetic variation.
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Affiliation(s)
- Alejandro Martin-Trujillo
- The Mindich Child Health and Development Institute and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Nihir Patel
- The Mindich Child Health and Development Institute and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Felix Richter
- The Mindich Child Health and Development Institute and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Bharati Jadhav
- The Mindich Child Health and Development Institute and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Paras Garg
- The Mindich Child Health and Development Institute and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sarah U. Morton
- Department of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - David M. McKean
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Steven R. DePalma
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Department of Pediatrics, University of Pennsylvania Perlman School of Medicine, Philadelphia, PA, United States of America
| | - Dorota Gruber
- Department of Pediatrics, Cohen Children’s Medical Center, Northwell Health, New Hyde Park, NY, Unites States of America
| | - Richard Kim
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jane W. Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - George A. Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States of America
| | | | - Daniel Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Martin Tristani-Firouzi
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States of America
| | - Jonathan G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christine E. Seidman
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts, United States of America
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, United States of America
| | - Bruce D. Gelb
- The Mindich Child Health and Development Institute and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Andrew J. Sharp
- The Mindich Child Health and Development Institute and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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41
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Trevino CE, Holleman AM, Corbitt H, Maslen CL, Rosser TC, Cutler DJ, Johnston HR, Rambo-Martin BL, Oberoi J, Dooley KJ, Capone GT, Reeves RH, Cordell HJ, Keavney BD, Agopian AJ, Goldmuntz E, Gruber PJ, O'Brien JE, Bittel DC, Wadhwa L, Cua CL, Moskowitz IP, Mulle JG, Epstein MP, Sherman SL, Zwick ME. Identifying genetic factors that contribute to the increased risk of congenital heart defects in infants with Down syndrome. Sci Rep 2020; 10:18051. [PMID: 33093519 PMCID: PMC7582922 DOI: 10.1038/s41598-020-74650-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/05/2020] [Indexed: 01/16/2023] Open
Abstract
Atrioventricular septal defects (AVSD) are a severe congenital heart defect present in individuals with Down syndrome (DS) at a > 2000-fold increased prevalence compared to the general population. This study aimed to identify risk-associated genes and pathways and to examine a potential polygenic contribution to AVSD in DS. We analyzed a total cohort of 702 individuals with DS with or without AVSD, with genomic data from whole exome sequencing, whole genome sequencing, and/or array-based imputation. We utilized sequence kernel association testing and polygenic risk score (PRS) methods to examine rare and common variants. Our findings suggest that the Notch pathway, particularly NOTCH4, as well as genes involved in the ciliome including CEP290 may play a role in AVSD in DS. These pathways have also been implicated in DS-associated AVSD in prior studies. A polygenic component for AVSD in DS has not been examined previously. Using weights based on the largest genome-wide association study of congenital heart defects available (2594 cases and 5159 controls; all general population samples), we found PRS to be associated with AVSD with odds ratios ranging from 1.2 to 1.3 per standard deviation increase in PRS and corresponding liability r2 values of approximately 1%, suggesting at least a small polygenic contribution to DS-associated AVSD. Future studies with larger sample sizes will improve identification and quantification of genetic contributions to AVSD in DS.
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Affiliation(s)
- Cristina E Trevino
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Aaron M Holleman
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Holly Corbitt
- Division of Cardiovascular Medicine and the Heart Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Cheryl L Maslen
- Division of Cardiovascular Medicine and the Heart Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Tracie C Rosser
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Benjamin L Rambo-Martin
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Jai Oberoi
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Kenneth J Dooley
- Sibley Heart Center Cardiology, Department of Pediatrics, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | | | - Roger H Reeves
- Department of Physiology and the Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - A J Agopian
- Human Genetics Center; Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, TX, USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter J Gruber
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - James E O'Brien
- The Ward Family Heart Center, Section of Cardiac Surgery, Children's Mercy Hospital, Kansas City, MO, USA
| | - Douglas C Bittel
- College of Biosciences, Kansas City University of Medicine and Biosciences, Kansas City, MO, USA
| | | | - Clifford L Cua
- Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Stephanie L Sherman
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
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42
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Sharma A, Wasson LK, Willcox JA, Morton SU, Gorham JM, DeLaughter DM, Neyazi M, Schmid M, Agarwal R, Jang MY, Toepfer CN, Ward T, Kim Y, Pereira AC, DePalma SR, Tai A, Kim S, Conner D, Bernstein D, Gelb BD, Chung WK, Goldmuntz E, Porter G, Tristani-Firouzi M, Srivastava D, Seidman JG, Seidman CE. GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm. eLife 2020; 9:53278. [PMID: 33054971 PMCID: PMC7593088 DOI: 10.7554/elife.53278] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 10/14/2020] [Indexed: 12/18/2022] Open
Abstract
Damaging GATA6 variants cause cardiac outflow tract defects, sometimes with pancreatic and diaphragmic malformations. To define molecular mechanisms for these diverse developmental defects, we studied transcriptional and epigenetic responses to GATA6 loss of function (LoF) and missense variants during cardiomyocyte differentiation of isogenic human induced pluripotent stem cells. We show that GATA6 is a pioneer factor in cardiac development, regulating SMYD1 that activates HAND2, and KDR that with HAND2 orchestrates outflow tract formation. LoF variants perturbed cardiac genes and also endoderm lineage genes that direct PDX1 expression and pancreatic development. Remarkably, an exon 4 GATA6 missense variant, highly associated with extra-cardiac malformations, caused ectopic pioneer activities, profoundly diminishing GATA4, FOXA1/2, and PDX1 expression and increasing normal retinoic acid signaling that promotes diaphragm development. These aberrant epigenetic and transcriptional signatures illuminate the molecular mechanisms for cardiovascular malformations, pancreas and diaphragm dysgenesis that arise in patients with distinct GATA6 variants.
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Affiliation(s)
- Arun Sharma
- Department of Genetics, Harvard Medical School, Boston, United States.,Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, United States.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, United States
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Jon Al Willcox
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Sarah U Morton
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Newborn Medicine, Boston Children's Hospital, Boston, United States
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, United States
| | | | - Meraj Neyazi
- Department of Genetics, Harvard Medical School, Boston, United States.,Hannover Medical School, Hannover, Germany
| | - Manuel Schmid
- Department of Genetics, Harvard Medical School, Boston, United States.,Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Radhika Agarwal
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Min Young Jang
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Christopher N Toepfer
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Alexandre C Pereira
- Department of Genetics, Harvard Medical School, Boston, United States.,Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, Brazil
| | - Steven R DePalma
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Angela Tai
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Seongwon Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - David Conner
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Wendy K Chung
- Department of Medicine, Columbia University Medical Center, New York, United States
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - George Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, United States
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, United States
| | | | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, United States
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43
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Nees SN, Chung WK. Genetic Basis of Human Congenital Heart Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036749. [PMID: 31818857 DOI: 10.1101/cshperspect.a036749] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Congenital heart disease (CHD) is the most common major congenital anomaly with an incidence of ∼1% of live births and is a significant cause of birth defect-related mortality. The genetic mechanisms underlying the development of CHD are complex and remain incompletely understood. Known genetic causes include all classes of genetic variation including chromosomal aneuploidies, copy number variants, and rare and common single-nucleotide variants, which can be either de novo or inherited. Among patients with CHD, ∼8%-12% have a chromosomal abnormality or aneuploidy, between 3% and 25% have a copy number variation, and 3%-5% have a single-gene defect in an established CHD gene with higher likelihood of identifying a genetic cause in patients with nonisolated CHD. These genetic variants disrupt or alter genes that play an important role in normal cardiac development and in some cases have pleiotropic effects on other organs. This work reviews some of the most common genetic causes of CHD as well as what is currently known about the underlying mechanisms.
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Affiliation(s)
| | - Wendy K Chung
- Department of Pediatrics.,Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
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44
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Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, Parfenov M, Homsy J, Gorham JM, Manheimer KB, Velinder M, Farrell A, Marth G, Schadt EE, Kaltman JR, Newburger JW, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter GA, Bernstein D, Chung WK, Srivastava D, Tristani-Firouzi M, Troyanskaya OG, Dickel DE, Shen Y, Seidman JG, Seidman CE, Gelb BD. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet 2020; 52:769-777. [PMID: 32601476 PMCID: PMC7415662 DOI: 10.1038/s41588-020-0652-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/22/2020] [Indexed: 02/07/2023]
Abstract
A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.
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Affiliation(s)
- Felix Richter
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alexander Kitaygorodsky
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hongjian Qi
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Nihir Patel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Center for External Innovation, Takeda Pharmaceuticals USA, Cambridge, MA, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kathryn B Manheimer
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Matthew Velinder
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrew Farrell
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Gabor Marth
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD, USA
| | | | | | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martina Brueckner
- Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Kim
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - George A Porter
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and University of California San Francisco, San Francisco, CA, USA
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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45
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Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, Morton SU, DePalma S, Gorham J, Kitaygorodksy A, Porter GA, Giardini A, Shen Y, Chung WK, Seidman JG, Seidman CE, Schadt EE, Gelb BD. ORE identifies extreme expression effects enriched for rare variants. Bioinformatics 2020; 35:3906-3912. [PMID: 30903145 DOI: 10.1093/bioinformatics/btz202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 01/13/2019] [Accepted: 03/20/2019] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Non-coding rare variants (RVs) may contribute to Mendelian disorders but have been challenging to study due to small sample sizes, genetic heterogeneity and uncertainty about relevant non-coding features. Previous studies identified RVs associated with expression outliers, but varying outlier definitions were employed and no comprehensive open-source software was developed. RESULTS We developed Outlier-RV Enrichment (ORE) to identify biologically-meaningful non-coding RVs. We implemented ORE combining whole-genome sequencing and cardiac RNAseq from congenital heart defect patients from the Pediatric Cardiac Genomics Consortium and deceased adults from Genotype-Tissue Expression. Use of rank-based outliers maximized sensitivity while a most extreme outlier approach maximized specificity. Rarer variants had stronger associations, suggesting they are under negative selective pressure and providing a basis for investigating their contribution to Mendelian disorders. AVAILABILITY AND IMPLEMENTATION ORE, source code, and documentation are available at https://pypi.python.org/pypi/ore under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- F Richter
- Graduate School of Biomedical Sciences
| | - G E Hoffman
- Icahn Institute for Genomics and Multiscale Biology.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - N Patel
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D McKean
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - S U Morton
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - S DePalma
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - J Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - A Kitaygorodksy
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - G A Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - A Giardini
- Cardiorespiratory Unit, Great Ormond Street Hospital and University College London, London, UK
| | - Y Shen
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - W K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - E E Schadt
- Icahn Institute for Genomics and Multiscale Biology.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, A Mount Sinai Venture, Stamford, CT, USA
| | - B D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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46
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Modeling Congenital Heart Disease Using Pluripotent Stem Cells. Curr Cardiol Rep 2020; 22:55. [PMID: 32562063 DOI: 10.1007/s11886-020-01316-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Congenital heart disease (CHD) represents a major class of birth defects worldwide and is associated with cardiac malformations that often require immediate surgery upon birth. Significant efforts are underway to better understand how CHD manifests through basic science approaches. Recently, human-induced pluripotent stem cells (hiPSCs) have emerged as a means by which to interrogate CHD phenotypes mechanistically. PURPOSE OF REVIEW: To review recent studies and results utilizing hiPSCs and their cardiovascular derivative cell types to better understand the mechanisms for various forms of CHD. RECENT FINDINGS: Recent studies demonstrate that hiPSC-derived cardiomyocytes can replicate the genetic and epigenetic abnormalities that ultimately lay the cellular foundation for CHD phenotypes. Such irregularities manifest in vitro through defects in hiPSC differentiation, signaling, and transcriptional activity. Use of hiPSC-derived cells to understand CHD may ultimately lead to the development of preemptive screening approaches to identify CHD early in utero and innovative therapies to alleviate symptoms after birth.
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47
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NOX2 Is Critical to Endocardial to Mesenchymal Transition and Heart Development. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:1679045. [PMID: 32655758 PMCID: PMC7320281 DOI: 10.1155/2020/1679045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/19/2020] [Accepted: 05/18/2020] [Indexed: 12/05/2022]
Abstract
NADPH oxidases (NOX) are a major source of reactive oxygen species (ROS) production in the heart. ROS signaling regulates gene expression, cell proliferation, apoptosis, and migration. However, the role of NOX2 in embryonic heart development remains elusive. We hypothesized that deficiency of Nox2 disrupts endocardial to mesenchymal transition (EndMT) and results in congenital septal and valvular defects. Our data show that 34% of Nox2−/− neonatal mice had various congenital heart defects (CHDs) including atrial septal defects (ASD), ventricular septal defects (VSD), atrioventricular canal defects (AVCD), and malformation of atrioventricular and aortic valves. Notably, Nox2−/− embryonic hearts show abnormal development of the endocardial cushion as evidenced by decreased cell proliferation and an increased rate of apoptosis. Additionally, Nox2 deficiency disrupted EndMT of atrioventricular cushion explants ex vivo. Furthermore, treatment with N-acetylcysteine (NAC) to reduce ROS levels in the wild-type endocardial cushion explants decreased the number of cells undergoing EndMT. Importantly, deficiency of Nox2 was associated with reduced expression of Gata4, Tgfβ2, Bmp2, Bmp4, and Snail1, which are critical to endocardial cushion and valvoseptal development. We conclude that NOX2 is critical to EndMT, endocardial cushion cell proliferation, and normal embryonic heart development.
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48
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Edwards JJ, Rouillard AD, Fernandez NF, Wang Z, Lachmann A, Shankaran SS, Bisgrove BW, Demarest B, Turan N, Srivastava D, Bernstein D, Deanfield J, Giardini A, Porter G, Kim R, Roberts AE, Newburger JW, Goldmuntz E, Brueckner M, Lifton RP, Seidman CE, Chung WK, Tristani-Firouzi M, Yost HJ, Ma'ayan A, Gelb BD. Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. JACC Basic Transl Sci 2020; 5:376-386. [PMID: 32368696 PMCID: PMC7188873 DOI: 10.1016/j.jacbts.2020.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/30/2022]
Abstract
Combining CHD phenotype–driven gene set enrichment and CRISPR knockdown screening in zebrafish is an effective approach to identifying novel CHD genes. Mutations affecting genes coding for the WAVE2 protein complex and small GTPase-mediated signaling are associated with LVOTO lesions. WAVE2 complex genes brk1, nckap1, and wasf2 and regulators of small GTPase signaling cul3a and racgap1 are critical to zebrafish heart development.
Genetic variants are the primary driver of congenital heart disease (CHD) pathogenesis. However, our ability to identify causative variants is limited. To identify causal CHD genes that are associated with specific molecular functions, the study used prior knowledge to filter de novo variants from 2,881 probands with sporadic severe CHD. This approach enabled the authors to identify an association between left ventricular outflow tract obstruction lesions and genes associated with the WAVE2 complex and regulation of small GTPase-mediated signal transduction. Using CRISPR zebrafish knockdowns, the study confirmed that WAVE2 complex proteins brk1, nckap1, and wasf2 and the regulators of small GTPase signaling cul3a and racgap1 are critical to cardiac development.
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Key Words
- CHD, congenital heart disease
- CORUM, Comprehensive Resource of Mammalian Protein Complexes
- CRISPR, clustered regularly interspaced short palindromic repeats
- CTD, conotruncal defect
- GOBP, Gene Ontology biological processes
- HHE, high heart expression
- HLHS, hypoplastic left heart syndrome
- HTX, heterotaxy
- LVOTO, left ventricular outflow tract obstruction
- MGI, Mouse Genome Informatics
- PCGC, Pediatric Cardiac Genomics Consortium
- PPI, protein-protein interaction
- congenital heart disease
- systems biology
- translational genomics
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Affiliation(s)
- Jonathan J Edwards
- Department of Pediatrics, Division of Pediatric Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew D Rouillard
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicolas F Fernandez
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sunita S Shankaran
- Department of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee
| | - Brent W Bisgrove
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | - Bradley Demarest
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, California
| | - Daniel Bernstein
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - John Deanfield
- Department of Cardiology, Great Ormond Street Hospital, University College London, London, United Kingdom
| | - Alessandro Giardini
- Department of Cardiology, Great Ormond Street Hospital, University College London, London, United Kingdom
| | - George Porter
- Department of Pediatrics, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Richard Kim
- Section of Cardiothoracic Surgery, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Amy E Roberts
- Department of Cardiology, Children's Hospital Boston, Boston, Massachusetts
| | - Jane W Newburger
- Department of Cardiology, Children's Hospital Boston, Boston, Massachusetts
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts.,Cardiovascular Division, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York.,Department of Medicine, Columbia University Medical Center, New York, New York
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - H Joseph Yost
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
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49
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Shi X, Zhang L, Bai K, Xie H, Shi T, Zhang R, Fu Q, Chen S, Lu Y, Yu Y, Sun K. Identification of rare variants in novel candidate genes in pulmonary atresia patients by next generation sequencing. Comput Struct Biotechnol J 2020; 18:381-392. [PMID: 32128068 PMCID: PMC7044470 DOI: 10.1016/j.csbj.2020.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 01/10/2020] [Accepted: 01/29/2020] [Indexed: 12/15/2022] Open
Abstract
Pulmonary atresia (PA) is a rare congenital heart defect (CHD) with complex manifestations and a high mortality rate. Since the genetic determinants in the pathogenesis of PA remain elusive, a thorough identification of the genetic factors through whole exome sequencing (WES) will provide novel insights into underlying mechanisms of PA. We performed WES data from PA/VSD (n = 60), PA/IVS (n = 20), TOF/PA (n = 20) and 100 healthy controls. Rare variants and novel genes were identified using variant-based association and gene-based burden analysis. Then we explored the expression pattern of our candidate genes in endothelium cell lines, pulmonary artery tissues, and embryonic hearts. 56 rare damage variants of 7 novel candidate genes (DNAH10, DST, FAT1, HMCN1, HNRNPC, TEP1, and TYK2) were certified to have function in PA pathogenesis for the first time. In our research, the genetic pattern among PA/VSD, PA/IVS and TOF/PA were different to some degree. Taken together, our findings contribute new insights into the molecular basis of this rare congenital birth defect.
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Key Words
- ACMG, American College of Medical Genetics
- CHD, congenital heart defect
- CTD, Conotruncal defect
- Congenital heart defect
- ExAC, Exome Aggregation Consortium
- FDR, False discovery rates
- GEO, Gene Expression Omnibus
- GSEA, gene set enrichment analysis
- Gene mutations
- HPAECs, Human Pulmonary Artery Endothelial Cells
- LOF, loss-of-function
- MAF, minor allele frequency
- PA, Pulmonary atresia
- PA/IVS, Pulmonary atresia with intact ventricular septum
- PA/VSD, Pulmonary atresia with ventricular septal defect
- PPI, protein–protein interactions
- Pulmonary atresia
- RT-qPCR, Reverse Transcription Quantitative PCR
- RV, right ventricle
- Rare variants
- SNP, single nucleotide polymorphism
- STRING, Search Tool for the Retrieval of Interacting Genes
- TOF, tetralogy of Fallot
- WES, whole exome sequencing
- Whole-exome sequencing
- gnomAD, Genome Aggregation Database
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Affiliation(s)
- Xin Shi
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Li Zhang
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science, East China Normal University, Ministry of Education, Shanghai, China
| | - Kai Bai
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Huilin Xie
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ruilin Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qihua Fu
- Medical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Sun Chen
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yanan Lu
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yu Yu
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China.,Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Kun Sun
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
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Seiden AH, Richter F, Patel N, Rodriguez OL, Deikus G, Shah H, Smith M, Roberts A, King EC, Sebra RP, Sharp AJ, Gelb BD. Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. Hum Mutat 2020; 41:800-806. [PMID: 31898844 DOI: 10.1002/humu.23971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/24/2019] [Accepted: 12/24/2019] [Indexed: 12/30/2022]
Abstract
The mechanisms underlying de novo insertion/deletion (indel) genesis, such as polymerase slippage, have been hypothesized but not well characterized in the human genome. We implemented two methodological improvements, which were leveraged to dissect indel mutagenesis. We assigned de novo variants to parent-of-origin (i.e., phasing) with low-coverage long-read whole-genome sequencing, achieving better phasing compared to short-read sequencing (medians of 84% and 23%, respectively). We then wrote an application programming interface to classify indels into three subtypes according to sequence context. Across three cohorts with different phasing methods (Ntrios = 540, all cohorts), we observed that one de novo indel subtype, change in copy count (CCC), was significantly correlated with father's (p = 7.1 × 10-4 ) but not mother's (p = .45) age at conception. We replicated this effect in three cohorts without de novo phasing (ppaternal = 1.9 × 10-9 , pmaternal = .61; Ntrios = 3,391, all cohorts). Although this is consistent with polymerase slippage during spermatogenesis, the percentage of variance explained by paternal age was low, and we did not observe an association with replication timing. These results suggest that spermatogenesis-specific events have a minor role in CCC indel mutagenesis, one not observed for other indel subtypes nor for maternal age in general. These results have implications for indel modeling in evolution and disease.
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Affiliation(s)
- Allison H Seiden
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Felix Richter
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nihir Patel
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Oscar L Rodriguez
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amy Roberts
- Division of Genetics, Department of Pediatrics and Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts
| | - Eileen C King
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew J Sharp
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
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