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Viswanathan S, Sandeep Oza P, Bellad A, Uttarilli A. Conotruncal Heart Defects: A Narrative Review of Molecular Genetics, Genomics Research and Innovation. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:324-346. [PMID: 38986083 DOI: 10.1089/omi.2024.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Congenital heart defects (CHDs) are most prevalent cardiac defects that occur at birth, leading to significant neonatal mortality and morbidity, especially in the developing nations. Among the CHDs, conotruncal heart defects (CTDs) are particularly noteworthy, comprising a significant portion of congenital cardiac anomalies. While advances in imaging and surgical techniques have improved the diagnosis, prognosis, and management of CTDs, their molecular genetics and genomic substrates remain incompletely understood. This expert review covers the recent advances from January 2016 onward and examines the complexities surrounding the genetic etiologies, prevalence, embryology, diagnosis, and clinical management of CTDs. We also emphasize the known copy number variants and single nucleotide variants associated with CTDs, along with the current planetary health research efforts aimed at CTDs in large cohort studies. In all, this comprehensive narrative review of molecular genetics and genomics research and innovation on CTDs draws from and highlights selected works from around the world and offers new ideas for advances in CTD diagnosis, precision medicine interventions, and accurate assessment of prognosis and recurrence risks.
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Affiliation(s)
- Sruthi Viswanathan
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prachi Sandeep Oza
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anikha Bellad
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anusha Uttarilli
- Institute of Bioinformatics, Bengaluru, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
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Yang D, Jian Z, Tang C, Chen Z, Zhou Z, Zheng L, Peng X. Zebrafish Congenital Heart Disease Models: Opportunities and Challenges. Int J Mol Sci 2024; 25:5943. [PMID: 38892128 PMCID: PMC11172925 DOI: 10.3390/ijms25115943] [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: 04/14/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Congenital heart defects (CHDs) are common human birth defects. Genetic mutations potentially cause the exhibition of various pathological phenotypes associated with CHDs, occurring alone or as part of certain syndromes. Zebrafish, a model organism with a strong molecular conservation similar to humans, is commonly used in studies on cardiovascular diseases owing to its advantageous features, such as a similarity to human electrophysiology, transparent embryos and larvae for observation, and suitability for forward and reverse genetics technology, to create various economical and easily controlled zebrafish CHD models. In this review, we outline the pros and cons of zebrafish CHD models created by genetic mutations associated with single defects and syndromes and the underlying pathogenic mechanism of CHDs discovered in these models. The challenges of zebrafish CHD models generated through gene editing are also discussed, since the cardiac phenotypes resulting from a single-candidate pathological gene mutation in zebrafish might not mirror the corresponding human phenotypes. The comprehensive review of these zebrafish CHD models will facilitate the understanding of the pathogenic mechanisms of CHDs and offer new opportunities for their treatments and intervention strategies.
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Roy P, Sah V, Deb N, Jaiswal V. Navigating the path of TOF- A Literature review unveiling maternal-fetal dynamics, treatment strategies and psychological dimensions. Dis Mon 2024; 70:101659. [PMID: 37951837 DOI: 10.1016/j.disamonth.2023.101659] [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] [Indexed: 11/14/2023]
Abstract
Tetralogy of Fallot (TOF) is a complex congenital heart defect that poses unique challenges for both mothers and their unborn children. This comprehensive review, aims to provide a holistic exploration of the maternal-fetal dynamics, treatment strategies, and psychological dimensions involved in navigating the path of TOF during pregnancy. It delves into the physiological changes that occur during pregnancy in TOF patients, including pulmonary regurgitation, right ventricular hypertrophy, and the overriding aorta. By understanding these dynamics, healthcare professionals can tailor treatment strategies to optimize maternal and fetal outcomes. The review further investigates the treatment strategies employed in managing TOF during pregnancy, encompassing medical interventions, cardiac monitoring, and multidisciplinary care. It explores the role of advanced imaging techniques, such as echocardiography and cardiac magnetic resonance imaging, in assessing TOF severity and guiding treatment decisions. The psychological factors influencing maternal adaptation, coping strategies, and the long-term implications on the child's psychological development are also examined. The integration of multidisciplinary approaches, including cardiac care, psychosocial support, and mental health interventions, can orchestrate a harmonious symphony of maternal-fetal well-being in the challenging journey of TOF pregnancies. Future research endeavours should continue to explore these dimensions, further refining treatment strategies and enhancing the understanding of TOF pregnancies for improved outcomes.
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Affiliation(s)
- Poulami Roy
- Department of Medicine, North Bengal Medical College and Hospital, India
| | - Viraj Sah
- Seth Gordhandas Sunderdas Medical College and King Edward Memorial Hospital, Mumbai
| | - Novonil Deb
- Department of Medicine, North Bengal Medical College and Hospital, India.
| | - Vikash Jaiswal
- Department of Cardiovascular Research, Larkin Community Hospital, South Miami, FL, USA
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Dorn C, Perrot A, Grunert M, Rickert-Sperling S. Human Genetics of Tetralogy of Fallot and Double-Outlet Right Ventricle. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:629-644. [PMID: 38884738 DOI: 10.1007/978-3-031-44087-8_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Tetralogy of Fallot (TOF) and double-outlet right ventricle (DORV) are conotruncal defects resulting from disturbances of the second heart field and the neural crest, which can occur as isolated malformations or as part of multiorgan syndromes. Their etiology is multifactorial and characterized by overlapping genetic causes. In this chapter, we present the different genetic alterations underlying the two diseases, which range from chromosomal abnormalities like aneuploidies and structural mutations to rare single nucleotide variations affecting distinct genes. For example, mutations in the cardiac transcription factors NKX2-5, GATA4, and HAND2 have been identified in isolated TOF cases, while mutations of TBX5 and 22q11 deletion, leading to haploinsufficiency of TBX1, cause Holt-Oram and DiGeorge syndrome, respectively. Moreover, genes involved in signaling pathways, laterality determination, and epigenetic mechanisms have also been found mutated in TOF and/or DORV patients. Finally, genome-wide association studies identified common single nucleotide polymorphisms associated with the risk for TOF.
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Affiliation(s)
- Cornelia Dorn
- Cardiovascular Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Perrot
- Cardiovascular Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel Grunert
- Cardiovascular Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
- DiNAQOR AG, Schlieren, Switzerland
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Bassett AS, Reuter MS, Malecki S, Silversides C, Oechslin E. Clinically Relevant Genetic Considerations for Patients With Tetralogy of Fallot. CJC PEDIATRIC AND CONGENITAL HEART DISEASE 2023; 2:426-439. [PMID: 38161665 PMCID: PMC10755827 DOI: 10.1016/j.cjcpc.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/05/2023] [Indexed: 01/03/2024]
Abstract
Genetic changes affect embryogenesis, cardiac and extracardiac phenotype, development, later onset conditions, and both short- and long-term outcomes and comorbidities in the increasing population of individuals with tetralogy of Fallot (TOF). In this review, we focus on current knowledge about clinically relevant genetics for patients with TOF across the lifespan. The latest findings for TOF genetics that are pertinent to day-to-day practice and lifelong management are highlighted: morbidity/mortality, cardiac/extracardiac features, including neurodevelopmental expression, and recent changes to prenatal screening and diagnostics. Genome-wide microarray is the first-line clinical genetic test for TOF across the lifespan, detecting relevant structural changes including the most common for TOF, the 22q11.2 microdeletion. Accumulating evidence illustrates opportunities for advances in understanding and care that may arise from genetic diagnosis at any age. We also glimpse into the near future when the multigenic nature of TOF will be more fully revealed, further enhancing possibilities for preventive care. Precision medicine is nigh.
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Affiliation(s)
- Anne S. Bassett
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, and Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
| | - Miriam S. Reuter
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Sarah Malecki
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Candice Silversides
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erwin Oechslin
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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Landis BJ, Helvaty LR, Geddes GC, Lin JI, Yatsenko SA, Lo CW, Border WL, Wechsler SB, Murali CN, Azamian MS, Lalani SR, Hinton RB, Garg V, McBride KL, Hodge JC, Ware SM. A Multicenter Analysis of Abnormal Chromosomal Microarray Findings in Congenital Heart Disease. J Am Heart Assoc 2023; 12:e029340. [PMID: 37681527 PMCID: PMC10547279 DOI: 10.1161/jaha.123.029340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/24/2023] [Indexed: 09/09/2023]
Abstract
Background Chromosomal microarray analysis (CMA) provides an opportunity to understand genetic causes of congenital heart disease (CHD). The methods for describing cardiac phenotypes in patients with CMA abnormalities have been inconsistent, which may complicate clinical interpretation of abnormal testing results and hinder a more complete understanding of genotype-phenotype relationships. Methods and Results Patients with CHD and abnormal clinical CMA were accrued from 9 pediatric cardiac centers. Highly detailed cardiac phenotypes were systematically classified and analyzed for their association with CMA abnormality. Hierarchical classification of each patient into 1 CHD category facilitated broad analyses. Inclusive classification allowing multiple CHD types per patient provided sensitive descriptions. In 1363 registry patients, 28% had genomic disorders with well-recognized CHD association, 67% had clinically reported copy number variants (CNVs) with rare or no prior CHD association, and 5% had regions of homozygosity without CNV. Hierarchical classification identified expected CHD categories in genomic disorders, as well as uncharacteristic CHDs. Inclusive phenotyping provided sensitive descriptions of patients with multiple CHD types, which occurred commonly. Among CNVs with rare or no prior CHD association, submicroscopic CNVs were enriched for more complex types of CHD compared with large CNVs. The submicroscopic CNVs that contained a curated CHD gene were enriched for left ventricular obstruction or septal defects, whereas CNVs containing a single gene were enriched for conotruncal defects. Neuronal-related pathways were over-represented in single-gene CNVs, including top candidate causative genes NRXN3, ADCY2, and HCN1. Conclusions Intensive cardiac phenotyping in multisite registry data identifies genotype-phenotype associations in CHD patients with abnormal CMA.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaya N. Murali
- Baylor College of MedicineHoustonTX
- Texas Children’s HospitalHoustonTX
| | | | - Seema R. Lalani
- Baylor College of MedicineHoustonTX
- Texas Children’s HospitalHoustonTX
| | | | - Vidu Garg
- Nationwide Children’s HospitalThe Ohio State UniversityColumbusOH
| | - Kim L. McBride
- Nationwide Children’s HospitalThe Ohio State UniversityColumbusOH
- University of CalgaryCalgaryCanada
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Hăşmăşanu MG, Procopciuc LM, Matyas M, Zonda GI, Zaharie GC. Genetic Polymorphisms of Vascular Endothelial Growth Factor in Neonatal Pathologies: A Systematic Search and Narrative Synthesis of the Literature. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10040744. [PMID: 37189993 DOI: 10.3390/children10040744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
(1) Background: Vascular endothelial growth factor (VEGF) is essential in vasculo- and angiogenesis due to its role in endothelial cell proliferation and migration. As a vascular proliferative factor, VEGF is one of the hallmarks of cancer and, in adult populations, the relationship between genetic polymorphism and neoplasm was widely investigated. For the neonatal population, only a few studies attempted to uncover the link between the genetic polymorphism of VEGF and neonatal pathology, especially related to late-onset complications. Our objective is to evaluate the literature surrounding VEGF genetic polymorphisms and the morbidity of the neonatal period. (2) Methods: A systematic search was initially conducted in December 2022. The PubMed platform was used to explore MEDLINE (1946 to 2022) and PubMed Central (2000 to 2022) by applying the search string ((VEGF polymorphism*) and newborn*). (3) Results: The PubMed search yielded 62 documents. A narrative synthesis of the findings was undertaken considering our predetermined subheadings (infants with low birth weight or preterm birth, heart pathologies, lung diseases, eye conditions, cerebral pathologies, and digestive pathologies). (4) Conclusion: The VEGF polymorphisms seem to be associated with neonatal pathology. The involvement of VEGF and VEGF polymorphism has been demonstrated for retinopathy of prematurity.
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Affiliation(s)
- Monica G Hăşmăşanu
- Department of Neonatology, Iuliu Haţieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Lucia M Procopciuc
- Department of Medical Biochemistry, Iuliu Haţieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Melinda Matyas
- Department of Neonatology, Iuliu Haţieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Gabriela I Zonda
- Department of Mother and Child Care, "Grigore T. Popa" University of Medicine and Pharmacy Iasi, 700115 Iași, Romania
| | - Gabriela C Zaharie
- Department of Neonatology, Iuliu Haţieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
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Verbitsky M, Krishnamurthy S, Krithivasan P, Hughes D, Khan A, Marasà M, Vena N, Khosla P, Zhang J, Lim TY, Glessner JT, Weng C, Shang N, Shen Y, Hripcsak G, Hakonarson H, Ionita-Laza I, Levy B, Kenny EE, Loos RJ, Kiryluk K, Sanna-Cherchi S, Crosslin DR, Furth S, Warady BA, Igo RP, Iyengar SK, Wong CS, Parsa A, Feldman HI, Gharavi AG. Genomic Disorders in CKD across the Lifespan. J Am Soc Nephrol 2023; 34:607-618. [PMID: 36302597 PMCID: PMC10103259 DOI: 10.1681/asn.2022060725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 01/24/2023] Open
Abstract
SIGNIFICANCE STATEMENT Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis. BACKGROUND Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility. METHODS We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II ( n =248), Chronic Renal Insufficiency Cohort (CRIC) study ( n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort. RESULTS We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk. CONCLUSION Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Pavan Khosla
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Junying Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Joseph T. Glessner
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology and Columbia Genome Center, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics and Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, 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
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David R. Crosslin
- Division of Biomedical Informatics and Genomics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Susan Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University and Louis Stoke, Cleveland, Ohio
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Afshin Parsa
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Medicine, Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Copy number variation-associated lncRNAs may contribute to the etiologies of congenital heart disease. Commun Biol 2023; 6:189. [PMID: 36806749 PMCID: PMC9938258 DOI: 10.1038/s42003-023-04565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Copy number variations (CNVs) have long been recognized as pathogenic factors for congenital heart disease (CHD). Few CHD associated CNVs could be interpreted as dosage effect due to disruption of coding sequences. Emerging evidences have highlighted the regulatory roles of long noncoding RNAs (lncRNAs) in cardiac development. Whereas it remains unexplored whether lncRNAs within CNVs (CNV-lncRNAs) could contribute to the etiology of CHD associated CNVs. Here we constructed coexpression networks involving CNV-lncRNAs within CHD associated CNVs and protein coding genes using the human organ developmental transcriptomic data, and showed that CNV-lncRNAs within 10 of the non-syndromic CHD associated CNVs clustered in the most significant heart correlated module, and had highly correlated coexpression with multiple key CHD genes. HSALNG0104472 within 15q11.2 region was identified as a hub CNV-lncRNA with heart-biased expression and validated experimentally. Our results indicated that HSALNG0104472 should be a main effector responsible for cardiac defects of 15q11.2 deletion through regulating cardiomyocytes differentiation. Our findings suggested that CNV-lncRNAs could potentially contribute to the pathologies of a maximum proportion of 68.4% (13/19) of non-syndromic CHD associated CNVs. These results indicated that explaining the pathogenesis of CHD associated CNVs should take account of the noncoding regions.
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10
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Ehrlich L, Prakash SK. Copy-number variation in congenital heart disease. Curr Opin Genet Dev 2022; 77:101986. [PMID: 36202051 DOI: 10.1016/j.gde.2022.101986] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/27/2023]
Abstract
Genomic copy-number variants (CNVs) contribute to as many congenital heart disease (CHD) cases (10-15%) as chromosomal aberrations or single-gene mutations and influence clinical outcomes. CNVs in a few genomic hotspots (1q21.1, 2q13, 8p23.1, 11q24, 15q11.2, 16p11.2, and 22q11.2) are recurrently enriched in CHD cohorts and affect dosage-sensitive transcriptional regulators that are required for cardiac development. Reduced penetrance and pleiotropic effects on brain and heart development are common features of these CNVs. Therefore, additional genetic 'hits,' such as a second CNV or gene mutation, are probably required to cause CHD in most cases. Integrative analysis of CNVs, genome sequence, epigenetic alterations, and gene function will be required to delineate the complete genetic landscape of CHD.
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Affiliation(s)
- Laurent Ehrlich
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Siddharth K Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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11
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Saacks NA, Eales J, Spracklen TF, Aldersley T, Human P, Verryn M, Lawrenson J, Cupido B, Comitis G, De Decker R, Fourie B, Swanson L, Joachim A, Brooks A, Ramesar R, Shaboodien G, Keavney BD, Zühlke LJ. Investigation of Copy Number Variation in South African Patients With Congenital Heart Defects. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2022; 15:e003510. [PMID: 36205932 PMCID: PMC9770125 DOI: 10.1161/circgen.121.003510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/27/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is a leading non-infectious cause of pediatric morbidity and mortality worldwide. Although the etiology of CHD is poorly understood, genetic factors including copy number variants (CNVs) contribute to the risk of CHD in individuals of European ancestry. The presence of rare CNVs in African CHD populations is unknown. This study aimed to identify pathogenic and likely pathogenic CNVs in South African patients with CHD. METHODS Genotyping was performed on 90 patients with nonsyndromic CHD using the Affymetrix CytoScan HD platform. These data were used to identify large, rare CNVs in known CHD-associated genes and candidate genes. RESULTS We identified eight CNVs overlapping known CHD-associated genes (GATA4, CRKL, TBX1, FLT4, B3GAT3, NSD1) in six patients. The analysis also revealed CNVs encompassing five candidate genes likely to play a role in the development of CHD (DGCR8, KDM2A, JARID2, FSTL1, CYFIP1) in five patients. One patient was found to have 47, XXY karyotype. We report a total discovery yield of 6.7%, with 5.6% of the cohort carrying pathogenic or likely pathogenic CNVs expected to cause the observed phenotypes. CONCLUSIONS In this study, we show that chromosomal microarray is an effective technique for identifying CNVs in African patients diagnosed with CHD and have demonstrated results similar to previous CHD genetic studies in Europeans. Novel potential CHD genes were also identified, indicating the value of genetic studies of CHD in ancestrally diverse populations.
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Affiliation(s)
- Nicole A. Saacks
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - James Eales
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom (J.E., B.D.K.)
| | - Timothy F. Spracklen
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
- Department of Medicine, Cape Heart Institute (T.F.S., G.S., L.J.Z.)
| | - Thomas Aldersley
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Paul Human
- Chris Barnard Division of Cardiothoracic Surgery, Department of Medicine, Faculty of Health Sciences (P.H., A.B.)
| | - Mark Verryn
- Cardiovascular Genetics Laboratory, Hatter Institute for Cardiovascular Research in Africa (M.V., G.S.)
| | - John Lawrenson
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health, University of Stellenbosch, Cape Town, South Africa (J.L., B.F.)
| | - Blanche Cupido
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, Faculty of Health Sciences (B.C., L.J.Z.)
| | - George Comitis
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Rik De Decker
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Barend Fourie
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health, University of Stellenbosch, Cape Town, South Africa (J.L., B.F.)
| | - Lenise Swanson
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Alexia Joachim
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
| | - Andre Brooks
- Chris Barnard Division of Cardiothoracic Surgery, Department of Medicine, Faculty of Health Sciences (P.H., A.B.)
| | - Raj Ramesar
- MRC Genomic & Precision Medicine Research Unit, Division of Human Genetics, Dept of Pathology, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa (R.R.)
| | - Gasnat Shaboodien
- Department of Medicine, Cape Heart Institute (T.F.S., G.S., L.J.Z.)
- Cardiovascular Genetics Laboratory, Hatter Institute for Cardiovascular Research in Africa (M.V., G.S.)
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom (J.E., B.D.K.)
| | - Liesl J. Zühlke
- Division of Pediatric Cardiology, Department of Pediatrics and Child Health (N.A.S., T.F.S., T.A., J.L., G.C., R.D.D., L.S., A.J., L.J.Z.)
- Department of Medicine, Cape Heart Institute (T.F.S., G.S., L.J.Z.)
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, Faculty of Health Sciences (B.C., L.J.Z.)
- South African Medical Research Council, Cape Town (L.J.Z.)
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12
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Hsieh T, Jin J. Loss of Calponin 2 causes age-progressive proteinuria in mice. Physiol Rep 2022; 10:e15370. [PMID: 36117313 PMCID: PMC9483440 DOI: 10.14814/phy2.15370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023] Open
Abstract
Proteinuria is a major manifestation of kidney disease, reflecting injuries of glomerular podocytes. Actin cytoskeleton plays a pivotal role in stabilizing the foot processes of podocytes against the hydrostatic pressure of filtration. Calponin is an actin associated protein that regulates mechanical tension-related cytoskeleton functions and its role in podocytes has not been established. Here we studied the kidney phenotypes of calponin isoform 2 knockout (KO) mice. Urine samples were examined to quantify the ratio of albumin and creatinine. Kidney tissue samples were collected for histology and ultrastructural studies. A mouse podocyte cell line (E11) was used to study the expression and cellular localization of calponin 2. In comparison with wild-type (WT) controls, calponin 2 KO mice showed age-progressive high proteinuria and degeneration of renal glomeruli. High levels of calponin 2 are expressed in E11 podocytes and colocalized with actin stress fibers, tropomyosin and myosin IIA. Electron microscopy showed that aging calponin 2 KO mice had effacement of the podocyte foot processes and increased thickness of the glomerular basement membrane as compared to that of WT control. The findings demonstrate that deletion of calponin 2 aggravates age-progressive degeneration of the glomerular structure and function as filtration barrier. The critical role of calponin 2 in podocytes suggests a molecular target for understanding the pathogenesis of proteinuria and therapeutic development.
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Affiliation(s)
- Tzu‐Bou Hsieh
- Department of Obstetrics & GynecologyWayne State University School of MedicineDetroitMichiganUSA
| | - Jian‐Ping Jin
- Department of Obstetrics & GynecologyWayne State University School of MedicineDetroitMichiganUSA
- Department of PhysiologyWayne State University School of MedicineDetroitMichiganUSA
- Department of Physiology and BiophysicsUniversity of Illinois at Chicago College of MedicineChicagoIllinoisUSA
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13
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Halabi R, Cechmanek PB, Hehr CL, McFarlane S. Semaphorin3f as a cardiomyocyte derived regulator of heart chamber development. Cell Commun Signal 2022; 20:126. [PMID: 35986301 PMCID: PMC9389736 DOI: 10.1186/s12964-022-00874-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 04/05/2022] [Indexed: 01/15/2023] Open
Abstract
Background During development a pool of precursors form a heart with atrial and ventricular chambers that exhibit distinct transcriptional and electrophysiological properties. Normal development of these chambers is essential for full term survival of the fetus, and deviations result in congenital heart defects. The large number of genes that may cause congenital heart defects when mutated, and the genetic variability and penetrance of the ensuing phenotypes, reveals a need to understand the molecular mechanisms that allow for the formation of chamber-specific cardiomyocyte differentiation. Methods We used in situ hybridization, immunohistochemistry and functional analyses to identify the consequences of the loss of the secreted semaphorin, Sema3fb, in the development of the zebrafish heart by using two sema3fb CRISPR mutant alleles. Results We find that in the developing zebrafish heart sema3fb mRNA is expressed by all cardiomyocytes, whereas mRNA for a known receptor Plexina3 (Plxna3) is expressed preferentially by ventricular cardiomyocytes. In sema3fb CRISPR zebrafish mutants, heart chamber development is impaired; the atria and ventricles of mutants are smaller in size than their wild type siblings, apparently because of differences in cell size and not cell numbers. Analysis of chamber differentiation indicates defects in chamber specific gene expression at the border between the ventricular and atrial chambers, with spillage of ventricular chamber genes into the atrium, and vice versa, and a failure to restrict specialized cardiomyocyte markers to the atrioventricular canal (AVC). The hypoplastic heart chambers are associated with decreased cardiac output and heart edema. Conclusions Based on our data we propose a model whereby cardiomyocytes secrete a Sema cue that, because of spatially restricted expression of the receptor, signals in a ventricular chamber-specific manner to establish a distinct border between atrial and ventricular chambers that is important to produce a fully functional heart. Video abstract
Supplementary information The online version contains supplementary material available at 10.1186/s12964-022-00874-8.
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14
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He GW, Maslen CL, Chen HX, Hou HT, Bai XY, Wang XL, Liu XC, Lu WL, Chen XX, Chen WD, Xing QS, Wu Q, Wang J, Yang Q. Identification of Novel Rare Copy Number Variants Associated with Sporadic Tetralogy of Fallot and Clinical Implications. Clin Genet 2022; 102:391-403. [PMID: 35882632 DOI: 10.1111/cge.14201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. Highly penetrant copy number variants (CNVs) and genes related to the etiology of TOF likely exist with differences among populations. We aimed to identify CNV contributions to sporadic TOF cases in Han Chinese. Genomic DNA was extracted from peripheral blood in 605 subjects (303 sporadic TOF and 302 unaffected Han Chinese [Control] from cardiac centers in China and analyzed by genome-wide association study (GWAS). The GWAS results were compared to existing Database of Genetic Variants. These CNVs were further validated by qPCR. Bioinformatics analyses were performed with Protein-Protein Interaction (PPI) network and KEGG pathway enrichment. Across all chromosomes 119 novel "TOF-specific CNVs" were identified with prevalence of CNVs of 21.5% in chromosomes 1-20 and 37.0% including Chr21/22. In chromosomes 1-20, CNVs on 11q25 (encompasses genes ACAD8, B3GAT1, GLB1L2, GLB1L3, IGSF9B, JAM3, LOC100128239, LOC283177, MIR4697, MIR4697HG, NCAPD3, OPCML, SPATA19, THYN1, and VPS26B) and 14q32.33 (encompasses genes THYN1, OPCML, and NCAPD3) encompass genes most likely to be associated with TOF. Specific CNVs found on the chromosome 21 (6.3%) and 22(11.9%) were also identified in details. PPI network analysis identified the genes covering the specific CNVs related to TOF and the signaling pathways. This study for first time identified novel TOF-specific CNVs in the Han Chinese with higher frequency than in Caucasians and with 11q25 and 14q32.33 not reported in TOF of Caucasians. These novel CNVs identify new candidate genes for TOF and provide new insights into genetic basis of TOF.
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Affiliation(s)
- Guo-Wei He
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China.,Department of Surgery, Oregon Health and Science University, Portland, Oregon, USA
| | - Cheryl L Maslen
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Huan-Xin Chen
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Hai-Tao Hou
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiao-Yan Bai
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiu-Li Wang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiao-Cheng Liu
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Wan-Li Lu
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xin-Xin Chen
- Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei-Dan Chen
- Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Quan-Sheng Xing
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Qin Wu
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Jun Wang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Qin Yang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
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15
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Reuter MS, Zech M, Hempel M, Altmüller J, Heung T, Pölsler L, Santer R, Thiele H, Trost B, Kubisch C, Scherer SW, Rudnik-Schöneborn S, Bassett AS, Lessel D. Biallelic PAN2 variants in individuals with a syndromic neurodevelopmental disorder and multiple congenital anomalies. Eur J Hum Genet 2022; 30:611-618. [PMID: 35304602 PMCID: PMC9090724 DOI: 10.1038/s41431-022-01077-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/10/2022] [Accepted: 02/17/2022] [Indexed: 12/26/2022] Open
Abstract
PAN2 encodes a subunit of a deadenylation complex with important functions in mRNA stability and post-transcriptional regulation of gene expression. A homozygous frameshift deletion in PAN2 was reported in a single affected individual with developmental delay and multiple congenital anomalies. Here, we describe five additional individuals from three unrelated families with homozygous predicted loss-of-function variants in PAN2. The affected individuals presented with significant overlap in their clinical features, including mild-moderate intellectual disability, hypotonia, sensorineural hearing loss, EEG abnormalities, congenital heart defects (tetralogy of Fallot, septal defects, dilated aortic root), urinary tract malformations, ophthalmological anomalies, short stature with other skeletal anomalies, and craniofacial features including flat occiput, ptosis, long philtrum, and short neck. Our data confirm that biallelic predicted loss-of-function variants in PAN2 cause a syndrome with multiple congenital anomalies, and suggest an important role of mRNA polyA tail length for proper organ formation.
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Affiliation(s)
- Miriam S Reuter
- CGEn, The Hospital for Sick Children, Toronto, ON, Canada.
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Laura Pölsler
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne and University Hospital Cologne, Cologne, Germany
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | | | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
- The Dalglish Family 22q Clinic for Adults with 22q11.2 Deletion Syndrome, Department of Psychiatry, and Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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Woodward AA, Taylor DM, Goldmuntz E, Mitchell LE, Agopian A, Moore JH, Urbanowicz RJ. Gene-Interaction-Sensitive enrichment analysis in congenital heart disease. BioData Min 2022; 15:4. [PMID: 35151364 PMCID: PMC8841104 DOI: 10.1186/s13040-022-00287-w] [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: 10/06/2021] [Accepted: 01/17/2022] [Indexed: 11/24/2022] Open
Abstract
Background Gene set enrichment analysis (GSEA) uses gene-level univariate associations to identify gene set-phenotype associations for hypothesis generation and interpretation. We propose that GSEA can be adapted to incorporate SNP and gene-level interactions. To this end, gene scores are derived by Relief-based feature importance algorithms that efficiently detect both univariate and interaction effects (MultiSURF) or exclusively interaction effects (MultiSURF*). We compare these interaction-sensitive GSEA approaches to traditional χ2 rankings in simulated genome-wide array data, and in a target and replication cohort of congenital heart disease patients with conotruncal defects (CTDs). Results In the simulation study and for both CTD datasets, both Relief-based approaches to GSEA captured more relevant and significant gene ontology terms compared to the univariate GSEA. Key terms and themes of interest include cell adhesion, migration, and signaling. A leading edge analysis highlighted semaphorins and their receptors, the Slit-Robo pathway, and other genes with roles in the secondary heart field and outflow tract development. Conclusions Our results indicate that interaction-sensitive approaches to enrichment analysis can improve upon traditional univariate GSEA. This approach replicated univariate findings and identified additional and more robust support for the role of the secondary heart field and cardiac neural crest cell migration in the development of CTDs. Supplementary Information The online version contains supplementary material available at (10.1186/s13040-022-00287-w).
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17
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Zhang X, Wang B, You G, Xiang Y, Fu Q, Yu Y, Zhang X. Copy number variation analysis in Chinese children with complete atrioventricular canal and single ventricle. BMC Med Genomics 2021; 14:243. [PMID: 34627233 PMCID: PMC8502261 DOI: 10.1186/s12920-021-01090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is one of the most common birth defects. Copy number variations (CNVs) have been proved to be important genetic factors that contribute to CHD. Here we screened genome-wide CNVs in Chinese children with complete atrioventricular canal (CAVC) and single ventricle (SV), since there were scarce researches dedicated to these two types of CHD. METHODS We screened CNVs in 262 sporadic CAVC cases and 259 sporadic SV cases respectively, using a customized SNP array. The detected CNVs were annotated and filtered using available databases. RESULTS Among 262 CAVC patients, we identified 6 potentially-causative CNVs in 43 individuals (16.41%, 43/262), including 2 syndrome-related CNVs (7q11.23 and 8q24.3 deletion). Surprisingly, 90.70% CAVC patients with detected CNVs (39/43) were found to carry duplications of 21q11.2-21q22.3, which were recognized as trisomy 21 (Down syndrome, DS). In CAVC with DS patients, the female to male ratio was 1.6:1.0 (24:15), and the rate of pulmonary hypertension (PH) was 41.03% (16/39). Additionally, 6 potentially-causative CNVs were identified in the SV patients (2.32%, 6/259), and none of them was trisomy 21. Most CNVs identified in our cohort were classified as rare (< 1%), occurring just once among CAVC or SV individuals except the 21q11.2-21q22.3 duplication (14.89%) in CAVC cohort. CONCLUSIONS Our study identified 12 potentially-causative CNVs in 262 CAVC and 259 SV patients, representing the largest cohort of these two CHD types in Chinese population. The results provided strong correlation between CAVC and DS, which also showed sex difference and high incidence of PH. The presence of potentially-causative CNVs suggests the etiology of complex CHD is incredibly diverse, and CHD candidate genes remain to be discovered.
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Affiliation(s)
- Xingyu Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoling You
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaoqing Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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18
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [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: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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19
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Reuter MS, Chaturvedi RR, Jobling RK, Pellecchia G, Hamdan O, Sung WW, Nalpathamkalam T, Attaluri P, Silversides CK, Wald RM, Marshall CR, Williams S, Keavney BD, Thiruvahindrapuram B, Scherer SW, Bassett AS. Clinical Genetic Risk Variants Inform a Functional Protein Interaction Network for Tetralogy of Fallot. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2021; 14:e003410. [PMID: 34328347 PMCID: PMC8373675 DOI: 10.1161/circgen.121.003410] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Tetralogy of Fallot (TOF)-the most common cyanotic heart defect in newborns-has evidence of multiple genetic contributing factors. Identifying variants that are clinically relevant is essential to understand patient-specific disease susceptibility and outcomes and could contribute to delineating pathomechanisms. METHODS Using a clinically driven strategy, we reanalyzed exome sequencing data from 811 probands with TOF, to identify rare loss-of-function and other likely pathogenic variants in genes associated with congenital heart disease. RESULTS We confirmed a major contribution of likely pathogenic variants in FLT4 (VEGFR3 [vascular endothelial growth factor receptor 3]; n=14) and NOTCH1 (n=10) and identified 1 to 3 variants in each of 21 other genes, including ATRX, DLL4, EP300, GATA6, JAG1, NF1, PIK3CA, RAF1, RASA1, SMAD2, and TBX1. In addition, multiple loss-of-function variants provided support for 3 emerging congenital heart disease/TOF candidate genes: KDR (n=4), IQGAP1 (n=3), and GDF1 (n=8). In total, these variants were identified in 63 probands (7.8%). Using the 26 composite genes in a STRING protein interaction enrichment analysis revealed a biologically relevant network (P=3.3×10-16), with VEGFR2 (vascular endothelial growth factor receptor 2; KDR) and NOTCH1 (neurogenic locus notch homolog protein 1) representing central nodes. Variants associated with arrhythmias/sudden death and heart failure indicated factors that could influence long-term outcomes. CONCLUSIONS The results are relevant to precision medicine for TOF. They suggest considerable clinical yield from genome-wide sequencing, with further evidence for KDR (VEGFR2) as a congenital heart disease/TOF gene and for VEGF (vascular endothelial growth factor) and Notch signaling as mechanisms in human disease. Harnessing the genetic heterogeneity of single gene defects could inform etiopathogenesis and help prioritize novel candidate genes for TOF.
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Affiliation(s)
- Miriam S. Reuter
- CGEn, Univ Health Network, Toronto, ON, Canada
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
- Program in Genetics & Genome Biology, Univ Health Network, Toronto, ON, Canada
| | - Rajiv R. Chaturvedi
- Labatt Family Heart Ctr, Univ Health Network, Toronto, ON, Canada
- Ontario Fetal Ctr, Mt Sinai Hospital, Univ Health Network, Toronto, ON, Canada
- Ted Rogers Ctr for Heart Rsrch, Cardiac Genome Clinic, Univ Health Network, Toronto, ON, Canada
| | - Rebekah K. Jobling
- Ted Rogers Ctr for Heart Rsrch, Cardiac Genome Clinic, Univ Health Network, Toronto, ON, Canada
- Division of Clinical & Metabolic Genetics, Univ Health Network, Toronto, ON, Canada
- Genome Diagnostics, Dept of Paediatric Laboratory Medicine, The Hospital for Sick Children, Univ Health Network, Toronto, ON, Canada
| | | | - Omar Hamdan
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
| | - Wilson W.L. Sung
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
| | | | - Pratyusha Attaluri
- Medical Genomics Program, Dept of Molecular Genetics, Univ Health Network, Toronto, ON, Canada
| | - Candice K. Silversides
- Division of Cardiology, Toronto Congenital Cardiac Ctr for Adults at the Peter Munk Cardiac Ctr, Dept of Medicine, Univ Health Network, Toronto, ON, Canada
| | - Rachel M. Wald
- Labatt Family Heart Ctr, Univ Health Network, Toronto, ON, Canada
- Division of Cardiology, Toronto Congenital Cardiac Ctr for Adults at the Peter Munk Cardiac Ctr, Dept of Medicine, Univ Health Network, Toronto, ON, Canada
| | - Christian R. Marshall
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
- Genome Diagnostics, Dept of Paediatric Laboratory Medicine, The Hospital for Sick Children, Univ Health Network, Toronto, ON, Canada
- Laboratory Medicine & Pathobiology, Univ Health Network, Toronto, ON, Canada
| | - Simon Williams
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine & Health, The Univ of Manchester, Manchester, UK
- Manchester Univ NHS Foundation Trust, Manchester Academic Health Science Ctr, Manchester, UK
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine & Health, The Univ of Manchester, Manchester, UK
- Manchester Univ NHS Foundation Trust, Manchester Academic Health Science Ctr, Manchester, UK
| | | | - Stephen W. Scherer
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
- Program in Genetics & Genome Biology, Univ Health Network, Toronto, ON, Canada
- Dept of Molecular Genetics, Univ Health Network, Toronto, ON, Canada
- McLaughlin Ctr, Univ Health Network, Toronto, ON, Canada
| | - Anne S. Bassett
- Division of Cardiology, Toronto Congenital Cardiac Ctr for Adults at the Peter Munk Cardiac Ctr, Dept of Medicine, Univ Health Network, Toronto, ON, Canada
- Clinical Genetics Research Program, Ctr for Addiction & Mental Health, Toronto, ON, Canada
- The Dalglish Family 22q Clinic for Adults with 22q11.2 Deletion Syndrome, Dept of Psychiatry & Toronto General Rsrch Inst, Univ Health Network, Toronto, ON, Canada
- Dept of Psychiatry, Univ of Toronto, Univ Health Network, Toronto, ON, Canada
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20
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Dyer LA, Rugonyi S. Fetal Blood Flow and Genetic Mutations in Conotruncal Congenital Heart Disease. J Cardiovasc Dev Dis 2021; 8:90. [PMID: 34436232 PMCID: PMC8397097 DOI: 10.3390/jcdd8080090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/19/2022] Open
Abstract
In congenital heart disease, the presence of structural defects affects blood flow in the heart and circulation. However, because the fetal circulation bypasses the lungs, fetuses with cyanotic heart defects can survive in utero but need prompt intervention to survive after birth. Tetralogy of Fallot and persistent truncus arteriosus are two of the most significant conotruncal heart defects. In both defects, blood access to the lungs is restricted or non-existent, and babies with these critical conditions need intervention right after birth. While there are known genetic mutations that lead to these critical heart defects, early perturbations in blood flow can independently lead to critical heart defects. In this paper, we start by comparing the fetal circulation with the neonatal and adult circulation, and reviewing how altered fetal blood flow can be used as a diagnostic tool to plan interventions. We then look at known factors that lead to tetralogy of Fallot and persistent truncus arteriosus: namely early perturbations in blood flow and mutations within VEGF-related pathways. The interplay between physical and genetic factors means that any one alteration can cause significant disruptions during development and underscore our need to better understand the effects of both blood flow and flow-responsive genes.
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Affiliation(s)
- Laura A. Dyer
- Department of Biology, University of Portland, Portland, OR 97203, USA;
| | - Sandra Rugonyi
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
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21
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Altuame FD, Shamseldin HE, Albatti TH, Hashem M, Ewida N, Abdulwahab F, Alkuraya FS. PLXNA2 as a candidate gene in patients with intellectual disability. Am J Med Genet A 2021; 185:3859-3865. [PMID: 34327814 DOI: 10.1002/ajmg.a.62440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 07/03/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
Intellectual disability (ID) is one of the most common disabilities in humans. In an effort to contribute to the expanding genetic landscape of ID, we describe a novel autosomal recessive ID candidate gene. Combined autozygome/exome analysis was performed in two unrelated consanguineous families with ID. Each of the two families had a novel homozygous likely deleterious variant in PLXNA2 and displayed the core phenotype of ID. PLXNA2 belongs to a family of transmembrane proteins that function as semaphorin receptors. Sema5A-PlexinA2 is known to regulate brain development in mouse, and Plxna2-/- mice display defective associative learning, sociability, and sensorimotor gating. We note the existence of variability in the phenotype among the three patients, including the existence of variable degree of ID, ranging from borderline intellectual functioning to moderate-severe ID, and the presence of cardiac anomalies in only one of the patients. We propose incomplete penetrance as a possible explanation of the observed difference in phenotypes. Future cases will be needed to support the proposed link between PLXNA2 and ID in humans.
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Affiliation(s)
- Fadie D Altuame
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Turki H Albatti
- Abdullatif Al Fozan Center for Autism, Alkhobar, Saudi Arabia.,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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22
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Diz OM, Toro R, Cesar S, Gomez O, Sarquella-Brugada G, Campuzano O. Personalized Genetic Diagnosis of Congenital Heart Defects in Newborns. J Pers Med 2021; 11:562. [PMID: 34208491 PMCID: PMC8235407 DOI: 10.3390/jpm11060562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 12/26/2022] Open
Abstract
Congenital heart disease is a group of pathologies characterized by structural malformations of the heart or great vessels. These alterations occur during the embryonic period and are the most frequently observed severe congenital malformations, the main cause of neonatal mortality due to malformation, and the second most frequent congenital malformations overall after malformations of the central nervous system. The severity of different types of congenital heart disease varies depending on the combination of associated anatomical defects. The causes of these malformations are usually considered multifactorial, but genetic variants play a key role. Currently, use of high-throughput genetic technologies allows identification of pathogenic aneuploidies, deletions/duplications of large segments, as well as rare single nucleotide variants. The high incidence of congenital heart disease as well as the associated complications makes it necessary to establish a diagnosis as early as possible to adopt the most appropriate measures in a personalized approach. In this review, we provide an exhaustive update of the genetic bases of the most frequent congenital heart diseases as well as other syndromes associated with congenital heart defects, and how genetic data can be translated to clinical practice in a personalized approach.
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Affiliation(s)
- Olga María Diz
- UGC Laboratorios, Hospital Universitario Puerta del Mar, 11009 Cadiz, Spain;
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08950 Barcelona, Spain
| | - Rocio Toro
- Medicine Department, School of Medicine, Cádiz University, 11519 Cadiz, Spain;
| | - Sergi Cesar
- Arrhythmia, Inherited Cardiac Diseases and Sudden Death Unit, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, University of Barcelona, 08007 Barcelona, Spain;
| | - Olga Gomez
- Fetal Medicine Research Center, BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08950 Barcelona, Spain;
- Centre for Biomedical Research on Rare Diseases (CIBER-ER), 28029 Madrid, Spain
| | - Georgia Sarquella-Brugada
- Arrhythmia, Inherited Cardiac Diseases and Sudden Death Unit, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, University of Barcelona, 08007 Barcelona, Spain;
- Medical Science Department, School of Medicine, University of Girona, 17003 Girona, Spain
| | - Oscar Campuzano
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08950 Barcelona, Spain
- Medical Science Department, School of Medicine, University of Girona, 17003 Girona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Cardiovasculares (CIBER-CV), 28029 Madrid, Spain
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23
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From Stem Cells to Populations-Using hiPSC, Next-Generation Sequencing, and GWAS to Explore the Genetic and Molecular Mechanisms of Congenital Heart Defects. Genes (Basel) 2021; 12:genes12060921. [PMID: 34208537 PMCID: PMC8235101 DOI: 10.3390/genes12060921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/01/2021] [Accepted: 06/12/2021] [Indexed: 01/16/2023] Open
Abstract
Congenital heart defects (CHD) are developmental malformations affecting the heart and the great vessels. Early heart development requires temporally regulated crosstalk between multiple cell types, signaling pathways, and mechanical forces of early blood flow. While both genetic and environmental factors have been recognized to be involved, identifying causal genes in non-syndromic CHD has been difficult. While variants following Mendelian inheritance have been identified by linkage analysis in a few families with multiple affected members, the inheritance pattern in most familial cases is complex, with reduced penetrance and variable expressivity. Furthermore, most non-syndromic CHD are sporadic. Improved sequencing technologies and large biobank collections have enabled genome-wide association studies (GWAS) in non-syndromic CHD. The ability to generate human to create human induced pluripotent stem cells (hiPSC) and further differentiate them to organotypic cells enables further exploration of genotype–phenotype correlations in patient-derived cells. Here we review how these technologies can be used in unraveling the genetics and molecular mechanisms of heart development.
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24
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Guida V, Sparascio FP, Bernardini L, Pancheri F, Melis D, Cocciadiferro D, Pagnoni M, Puzzo M, Goldoni M, Barone C, Hozhabri H, Putotto C, Giuffrida MG, Briuglia S, Palumbo O, Bianca S, Stanzial F, Benedicenti F, Kariminejad A, Forzano F, Baghernajad Salehi L, Mattina T, Brancati F, Castori M, Carella M, Fadda MT, Iannetti G, Dallapiccola B, Digilio MC, Marino B, Tartaglia M, De Luca A. Copy number variation analysis implicates novel pathways in patients with oculo-auriculo-vertebral-spectrum and congenital heart defects. Clin Genet 2021; 100:268-279. [PMID: 33988253 DOI: 10.1111/cge.13994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/22/2021] [Accepted: 05/08/2021] [Indexed: 12/19/2022]
Abstract
Oculo-auriculo-vertebral spectrum (OAVS) is a developmental disorder of craniofacial morphogenesis. Its etiology is unclear, but assumed to be complex and heterogeneous, with contribution of both genetic and environmental factors. We assessed the occurrence of copy number variants (CNVs) in a cohort of 19 unrelated OAVS individuals with congenital heart defect. Chromosomal microarray analysis identified pathogenic CNVs in 2/19 (10.5%) individuals, and CNVs classified as variants of uncertain significance in 7/19 (36.9%) individuals. Remarkably, two subjects had small intragenic CNVs involving DACH1 and DACH2, two paralogs coding for key components of the PAX-SIX-EYA-DACH network, a transcriptional regulatory pathway controlling developmental processes relevant to OAVS and causally associated with syndromes characterized by craniofacial involvement. Moreover, a third patient showed a large duplication encompassing DMBX1/OTX3, encoding a transcriptional repressor of OTX2, another transcription factor functionally connected to the DACH-EYA-PAX network. Among the other relevant CNVs, a deletion encompassing HSD17B6, a gene connected with the retinoic acid signaling pathway, whose dysregulation has been implicated in craniofacial malformations, was also identified. Our findings suggest that CNVs affecting gene dosage likely contribute to the genetic heterogeneity of OAVS, and implicate the PAX-SIX-EYA-DACH network as novel pathway involved in the etiology of this developmental trait.
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Affiliation(s)
- Valentina Guida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesca Piceci Sparascio
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.,Department of Experimental Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Laura Bernardini
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesco Pancheri
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Daniela Melis
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Naples, Italy.,Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Dario Cocciadiferro
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.,Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mario Pagnoni
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Marianna Puzzo
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marina Goldoni
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Chiara Barone
- Medical Genetics, Referral Center for Rare Genetic Diseases, ARNAS Garibaldi, Catania, Italy
| | - Hossein Hozhabri
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Carolina Putotto
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Maria Grazia Giuffrida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Silvana Briuglia
- Department of Human Pathology of Adult and Childhood "Gaetano Barresi", Unit of Emergency Pediatrics, University of Messina, Messina, Italy
| | - Orazio Palumbo
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Sebastiano Bianca
- Medical Genetics, Referral Center for Rare Genetic Diseases, ARNAS Garibaldi, Catania, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Francesca Forzano
- Clinical Genetics Department, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | | | - Teresa Mattina
- Unit of Medical Genetics, University of Catania, Catania, Italy
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, Unit of Medical Genetics University of L'Aquila, L'Aquila, Italy
| | - Marco Castori
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Massimo Carella
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Teresa Fadda
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Giorgio Iannetti
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Bruno Marino
- Department of Pediatrics, Obstetrics and Gynecology, "Sapienza" University of Rome, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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25
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Blagojevic C, Heung T, van Mil S, Oechslin E, Silversides CK, Granton JT, Bassett AS. Abnormal spirometry in adults with 22q11.2 microdeletion and congenital heart disease. INTERNATIONAL JOURNAL OF CARDIOLOGY CONGENITAL HEART DISEASE 2021. [DOI: 10.1016/j.ijcchd.2021.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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26
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Wu Y, Jin X, Zhang Y, Zheng J, Yang R. Genetic and epigenetic mechanisms in the development of congenital heart diseases. WORLD JOURNAL OF PEDIATRIC SURGERY 2021; 4:e000196. [DOI: 10.1136/wjps-2020-000196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common of congenital cardiovascular malformations associated with birth defects, and it results in significant morbidity and mortality worldwide. The classification of CHD is still elusive owing to the complex pathogenesis of CHD. Advances in molecular medicine have revealed the genetic basis of some heart anomalies. Genes associated with CHD might be modulated by various epigenetic factors. Thus, the genetic and epigenetic factors are gradually accepted as important triggers in the pathogenesis of CHD. However, few literatures have comprehensively elaborated the genetic and epigenetic mechanisms of CHD. This review focuses on the etiology of CHD from genetics and epigenetics to discuss the role of these factors in the development of CHD. The interactions between genetic and epigenetic in the pathogenesis of CHD are also elaborated. Chromosome abnormalities and gene mutations in genetics, and DNA methylations, histone modifications and on-coding RNAs in epigenetics are summarized in detail. We hope the summative knowledge of these etiologies may be useful for improved diagnosis and further elucidation of CHD so that morbidity and mortality of children with CHD can be reduced in the near future.
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Abstract
The developing heart is formed of two tissue layers separated by an extracellular matrix (ECM) that provides chemical and physical signals to cardiac cells. While deposition of specific ECM components creates matrix diversity, the cardiac ECM is also dynamic, with modification and degradation playing important roles in ECM maturation and function. In this Review, we discuss the spatiotemporal changes in ECM composition during cardiac development that support distinct aspects of heart morphogenesis. We highlight conserved requirements for specific ECM components in human cardiac development, and discuss emerging evidence of a central role for the ECM in promoting heart regeneration.
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Affiliation(s)
| | - Emily S Noël
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
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28
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Zhang H, Yue F, Zhang X, He J, Jiang Y, Liu R, Yu Y. Prenatal detection of distal 1q21.1q21.2 microduplication with abnormal ultrasound findings: Two cases report and literature review. Medicine (Baltimore) 2021; 100:e24227. [PMID: 33429818 PMCID: PMC7793324 DOI: 10.1097/md.0000000000024227] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/17/2020] [Indexed: 01/05/2023] Open
Abstract
RATIONALE 1q21.1 duplication is an uncommon chromosomal submicroscopic imbalance which is associated with growth/mental retardation, dysmorphic features, autism, multiple congenital and neuropsychiatric disorders. PATIENT CONCERNS Two pregnant women underwent amniocentesis for cytogenetic analysis and chromosomal microarray analysis (CMA) following abnormal ultrasound findings. Case 1 presented short nasal bone and case 2 showed absent nasal bone, ventricular septal defect and umbilical cord circling in ultrasonic examination. DIAGNOSES G-banding analysis showed that the two fetuses presented normal karyotypic results while CMA detected 1.796 Mb (case 1) and 1.242 Mb (case 2) microduplications in the region of 1q21.1q21.2 separately. Furthermore, the CMA also revealed a 1.2 Mb microdeletion of 8p23.3 in case 1. INTERVENTIONS The couple in case 1 chose to terminate the pregnancy, while the couple in case 2 continued the pregnancy and finally delivered a male infant who presented low nasal bridge and ventricular septal defect. OUTCOMES The 1q21.1q21.2 duplications in our report were located in the distal 1q21.1 region, overlapping with 1q21.1 duplication syndrome. Case 2 was the first reported live birth with 1q21.1 duplication according to prenatal CMA detection in China. LESSONS The genotype-phenotype of 1q21.1 duplication is complicated due to the phenotypic diversity, incomplete penetrance, and lack of obvious characteristics. So it is difficult to predict the postnatal development and health conditions clinically. Hence, long term follow up is necessary for newborn infants with 1q21.1 duplication, irrespective of whether the duplication is de novo or inherited.
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Affiliation(s)
- Hongguo Zhang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Fagui Yue
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Xinyue Zhang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Jing He
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Yuting Jiang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ruizhi Liu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Yang Yu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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29
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Grunert M, Appelt S, Grossfeld P, Sperling SR. The Needle in the Haystack-Searching for Genetic and Epigenetic Differences in Monozygotic Twins Discordant for Tetralogy of Fallot. J Cardiovasc Dev Dis 2020; 7:jcdd7040055. [PMID: 33276527 PMCID: PMC7761217 DOI: 10.3390/jcdd7040055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
Congenital heart defects (CHDs) are the most common birth defect in human with an incidence of almost 1% of all live births. Most cases have a multifactorial origin with both genetics and the environment playing a role in its development and progression. Adding an epigenetic component to this aspect is exemplified by monozygotic twins which share the same genetic background but have a different disease status. As a result, the interplay between the genetic, epigenetic and the environmental conditions might contribute to the etiology and phenotype. To date, the underlying causes of the majority of CHDs remain poorly understood. In this study, we performed genome-wide high-throughput sequencing to examine the genetic, structural genomic and epigenetic differences of two identical twin pairs discordant for Tetralogy of Fallot (TOF), representing the most common cyanotic form of CHDs. Our results show the almost identical genetic and structural genomic identity of the twins. In contrast, several epigenetic alterations could be observed given by DNA methylation changes in regulatory regions of known cardiac-relevant genes. Overall, this study provides first insights into the impact of genetic and especially epigenetic factors underlying monozygotic twins discordant for CHD like TOF.
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Affiliation(s)
- Marcel Grunert
- Cardiovascular Genetics, Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany; (M.G.); (S.A.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10178 Berlin, Germany
| | - Sandra Appelt
- Cardiovascular Genetics, Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany; (M.G.); (S.A.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10178 Berlin, Germany
| | - Paul Grossfeld
- Division of Cardiology, University of California San Diego, Rady’s Hospital MC 5004, San Diego, CA 92123, USA;
| | - Silke R. Sperling
- Cardiovascular Genetics, Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany; (M.G.); (S.A.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10178 Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Correspondence: ; Tel.: +49-30450540123
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30
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Lee C, Cox RM, Papoulas O, Horani A, Drew K, Devitt CC, Brody SL, Marcotte EM, Wallingford JB. Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins. eLife 2020; 9:e58662. [PMID: 33263282 PMCID: PMC7785291 DOI: 10.7554/elife.58662] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022] Open
Abstract
Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly-acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles). Here, we use in vivo imaging in Xenopus to show that inner dynein arm (IDA) and outer dynein arm (ODA) subunits are partitioned into non-overlapping sub-regions within DynAPs. Using affinity- purification mass-spectrometry of in vivo interaction partners, we also identify novel partners for inner and outer dynein arms. Among these, we identify C16orf71/Daap1 as a novel axonemal dynein regulator. Daap1 interacts with ODA subunits, localizes specifically to the cytoplasm, is enriched in DynAPs, and is required for the deployment of ODAs to axonemes. Our work reveals a new complexity in the structure and function of a cell-type specific liquid-like organelle that is directly relevant to human genetic disease.
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Affiliation(s)
- Chanjae Lee
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Rachael M Cox
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Ophelia Papoulas
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Amjad Horani
- Department of Pediatrics, Washington University School of MedicineSt. LouisUnited States
| | - Kevin Drew
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Caitlin C Devitt
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - Steven L Brody
- Department of Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of TexasAustinUnited States
| | - John B Wallingford
- Department of Molecular Biosciences, University of TexasAustinUnited States
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31
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Qian Z, Van den Eynde J, Heymans S, Mertens L, Morava E. Vascular ring anomaly in a patient with phosphomannomutase 2 deficiency: A case report and review of the literature. JIMD Rep 2020; 56:27-33. [PMID: 33204593 PMCID: PMC7653259 DOI: 10.1002/jmd2.12160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Congenital disorders of glycosylation (CDG) are a group of metabolic disorders well known to be associated with developmental delay and central nervous system anomalies. The most common CDG is caused by pathogenic variants in the phosphomannomutase 2 gene (PMM2), which impairs one of the first steps of N-glycosylation and affects multiple organ systems. Cardiac involvement can include pericardial effusion, cardiomyopathy, and arrhythmia, while an association with cardiovascular congenital anomalies is not well studied. CASE SUMMARY We report a 6-year-old individual who initially presented with inverted nipples, developmental delay, and failure to thrive at 3 months of age. At 4 months, due to feeding problems, swallowing exam and echocardiography were performed which revealed a vascular ring anomaly based on a right aortic arch and aberrant left subclavian artery. Subsequent whole exome gene sequencing revealed two pathogenic PMM2-CDG variants (E139K/R141H) and no known pathogenic mutations related to congenital heart defect (CHD). DISCUSSION This is the first report of vascular ring anomaly in a patient with PMM2-CDG. We conducted a literature review of PMM2-CDG patients with reported CHD. Of the 14 patients with PMM2-CDG and cardiac malformation, the most common CHD's were tetralogy of Fallot, patent ductus arteriosus, and truncus arteriosus. The potential important link between CDG and CHD is stressed and discussed. Furthermore, the importance of multidisciplinary care for CDG patients including early referral to pediatric cardiologists is highlighted.
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Affiliation(s)
- Zhen Qian
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
- Research Group Experimental Oto‐Rhino‐LaryngologyKU LeuvenLeuvenBelgium
- Faculty of MedicineKU LeuvenLeuvenBelgium
| | - Jef Van den Eynde
- Faculty of MedicineKU LeuvenLeuvenBelgium
- Labatt Family Heart Center, Department of PaediatricsHospital for Sick Children and University of TorontoTorontoOntarioCanada
- Department of Cardiovascular SciencesKU LeuvenLeuvenBelgium
| | - Stephane Heymans
- Department of Cardiovascular SciencesKU LeuvenLeuvenBelgium
- Cardiovascular Research Institute Maastricht (CARIM)Maastricht UniversityMaastrichtThe Netherlands
- Netherlands Heart Institute (ICIN)UtrechtThe Netherlands
| | - Luc Mertens
- Labatt Family Heart Center, Department of PaediatricsHospital for Sick Children and University of TorontoTorontoOntarioCanada
| | - Eva Morava
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
- Faculty of MedicineKU LeuvenLeuvenBelgium
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32
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Manshaei R, Merico D, Reuter MS, Engchuan W, Mojarad BA, Chaturvedi R, Heung T, Pellecchia G, Zarrei M, Nalpathamkalam T, Khan R, Okello JBA, Liston E, Curtis M, Yuen RKC, Marshall CR, Jobling RK, Oechslin E, Wald RM, Silversides CK, Scherer SW, Kim RH, Bassett AS. Genes and Pathways Implicated in Tetralogy of Fallot Revealed by Ultra-Rare Variant Burden Analysis in 231 Genome Sequences. Front Genet 2020; 11:957. [PMID: 33110418 PMCID: PMC7522597 DOI: 10.3389/fgene.2020.00957] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Recent genome-wide studies of rare genetic variants have begun to implicate novel mechanisms for tetralogy of Fallot (TOF), a severe congenital heart defect (CHD). To provide statistical support for case-only data without parental genomes, we re-analyzed genome sequences of 231 individuals with TOF (n = 175) or related CHD. We adapted a burden test originally developed for de novo variants to assess ultra-rare variant burden in individual genes, and in gene-sets corresponding to functional pathways and mouse phenotypes, accounting for highly correlated gene-sets and for multiple testing. For truncating variants, the gene burden test confirmed significant burden in FLT4 (Bonferroni corrected p-value < 0.01). For missense variants, burden in NOTCH1 achieved genome-wide significance only when restricted to constrained genes (i.e., under negative selection, Bonferroni corrected p-value = 0.004), and showed enrichment for variants affecting the extracellular domain, especially those disrupting cysteine residues forming disulfide bonds (OR = 39.8 vs. gnomAD). Individuals with NOTCH1 ultra-rare missense variants, all with TOF, were enriched for positive family history of CHD. Other genes not previously implicated in CHD had more modest statistical support in gene burden tests. Gene-set burden tests for truncating variants identified a cluster of pathways corresponding to VEGF signaling (FDR = 0%), and of mouse phenotypes corresponding to abnormal vasculature (FDR = 0.8%); these suggested additional candidate genes not previously identified (e.g., WNT5A and ZFAND5). Results for the most promising genes were driven by the TOF subset of the cohort. The findings support the importance of ultra-rare variants disrupting genes involved in VEGF and NOTCH signaling in the genetic architecture of TOF, accounting for 11–14% of individuals in the TOF cohort. These proof-of-principle data indicate that this statistical methodology could assist in analyzing case-only sequencing data in which ultra-rare variants, whether de novo or inherited, contribute to the genetic etiopathogenesis of a complex disorder.
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Affiliation(s)
- Roozbeh Manshaei
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daniele Merico
- Deep Genomics Inc., Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bahareh A Mojarad
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rajiv Chaturvedi
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Labatt Heart Centre, Division of Cardiology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.,The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Reem Khan
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - John B A Okello
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eriskay Liston
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Meredith Curtis
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rebekah K Jobling
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Erwin Oechslin
- Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Rachel M Wald
- Labatt Heart Centre, Division of Cardiology, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Candice K Silversides
- Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Raymond H Kim
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.,The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada.,Division of Cardiology, Toronto Congenital Cardiac Centre for Adults at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Department of Mental Health, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
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33
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Williams SG, Nakev A, Guo H, Frain S, Tenin G, Liakhovitskaia A, Saha P, Priest JR, Hentges KE, Keavney BD. Association of congenital cardiovascular malformation and neuropsychiatric phenotypes with 15q11.2 (BP1-BP2) deletion in the UK Biobank. Eur J Hum Genet 2020; 28:1265-1273. [PMID: 32327713 PMCID: PMC7608352 DOI: 10.1038/s41431-020-0626-8] [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: 09/03/2019] [Revised: 02/12/2020] [Accepted: 03/24/2020] [Indexed: 12/28/2022] Open
Abstract
Deletion of a non-imprinted 500kb genomic region at chromosome 15q11.2, between breakpoints 1 and 2 of the Prader-Willi/Angelman locus (BP1-BP2 deletion), has been associated in previous studies with phenotypes including congenital cardiovascular malformations (CVM). Previous studies investigating association between BP1-BP2 deletion and CVM have tended to recruit cases with rarer and more severe CVM phenotypes; the impact of CVM on relatively unselected population cohorts, anticipated to contain chiefly less severe but commoner CHD phenotypes, is relatively unexplored. More precisely defining the impact of BP1-BP2 deletion on CVM risk could be useful to guide genetic counselling, since the deletion is frequently identified in the neurodevelopmental clinic. Using the UK Biobank (UKB) cohort of ~500,000 individuals, we identified individuals with CVM and investigated the association with deletions at the BP1-BP2 locus. In addition, we assessed the association of BP1-BP2 deletions with neuropsychiatric diagnoses, cognitive function and academic achievement. Cases of CVM had an increased prevalence of the deletion compared with controls (0.64%; OR = 1.73 [95% CI 1.08-2.75]; p = 0.03), as did those with neuropsychiatric diagnoses (0.68%; OR = 1.84 [95% CI 1.23-2.75]; p = 0.004). We conclude that BP1-BP2 deletion moderately increases the risk of the generally milder, but commoner, CVM phenotypes seen in this unselected population, in addition to its previously demonstrated association in case/control studies ascertained for CVM.
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Affiliation(s)
- Simon G Williams
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Apostol Nakev
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Hui Guo
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Simon Frain
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Gennadiy Tenin
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Anna Liakhovitskaia
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Priyanka Saha
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - James R Priest
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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Ortinau CM, Shimony JS. The Congenital Heart Disease Brain: Prenatal Considerations for Perioperative Neurocritical Care. Pediatr Neurol 2020; 108:23-30. [PMID: 32107137 PMCID: PMC7306416 DOI: 10.1016/j.pediatrneurol.2020.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/21/2019] [Accepted: 01/05/2020] [Indexed: 12/17/2022]
Abstract
Altered brain development has been highlighted as an important contributor to adverse neurodevelopmental outcomes in children with congenital heart disease. Abnormalities begin prenatally and include micro- and macrostructural disturbances that lead to an altered trajectory of brain growth throughout gestation. Recent progress in fetal imaging has improved understanding of the neurobiological mechanisms and risk factors for impaired fetal brain development. The impact of the prenatal environment on postnatal neurological care has also gained increased focus. This review summarizes current data on the timing and pattern of altered prenatal brain development in congenital heart disease, the potential mechanisms of these abnormalities, and the association with perioperative neurological complications.
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Affiliation(s)
- Cynthia M Ortinau
- Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri.
| | - Joshua S Shimony
- Mallinkrodt Institute of Radiology, Washington University in St. Louis, St. Louis, Missouri
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35
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Boskovski MT, Homsy J, Nathan M, Sleeper LA, Morton S, Manheimer KB, Tai A, Gorham J, Lewis M, Swartz M, Alfieris GM, Bacha EA, Karimi M, Meyer D, Nguyen K, Bernstein D, Romano-Adesman A, Porter GA, Goldmuntz E, Chung WK, Srivastava D, Kaltman JR, Tristani-Firouzi M, Lifton R, Roberts AE, Gaynor JW, Gelb BD, Kim R, Seidman JG, Brueckner M, Mayer JE, Newburger JW, Seidman CE. De Novo Damaging Variants, Clinical Phenotypes, and Post-Operative Outcomes in Congenital Heart Disease. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 13:e002836. [PMID: 32812804 PMCID: PMC7439931 DOI: 10.1161/circgen.119.002836] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Supplemental Digital Content is available in the text. Background: De novo genic and copy number variants are enriched in patients with congenital heart disease, particularly those with extra-cardiac anomalies. The impact of de novo damaging variants on outcomes following cardiac repair is unknown. Methods: We studied 2517 patients with congenital heart disease who had undergone whole-exome sequencing as part of the CHD GENES study (Congenital Heart Disease Genetic Network). Results: Two hundred ninety-four patients (11.7%) had clinically significant de novo variants. Patients with de novo damaging variants were 2.4 times more likely to have extra-cardiac anomalies (P=5.63×10−12). In 1268 patients (50.4%) who had surgical data available and underwent open-heart surgery exclusive of heart transplantation as their first operation, we analyzed transplant-free survival following the first operation. Median follow-up was 2.65 years. De novo variants were associated with worse transplant-free survival (hazard ratio, 3.51; P=5.33×10−04) and longer times to final extubation (hazard ratio, 0.74; P=0.005). As de novo variants had a significant interaction with extra-cardiac anomalies for transplant-free survival (P=0.003), de novo variants conveyed no additional risk for transplant-free survival for patients with these anomalies (adjusted hazard ratio, 1.96; P=0.06). By contrast, de novo variants in patients without extra-cardiac anomalies were associated with worse transplant-free survival during follow-up (hazard ratio, 11.21; P=1.61×10−05) than that of patients with no de novo variants. Using agnostic machine-learning algorithms, we identified de novo copy number variants at 15q25.2 and 15q11.2 as being associated with worse transplant-free survival and 15q25.2, 22q11.21, and 3p25.2 as being associated with prolonged time to final extubation. Conclusions: In patients with congenital heart disease undergoing open-heart surgery, de novo variants were associated with worse transplant-free survival and longer times on the ventilator. De novo variants were most strongly associated with adverse outcomes among patients without extra-cardiac anomalies, suggesting a benefit for preoperative genetic testing even when genetic abnormalities are not suspected during routine clinical practice. Registration: URL: https://www.clinicaltrials.gov. Unique identifier: NCT01196182.
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Affiliation(s)
- Marko T Boskovski
- Department of Cardiac Surgery (M.T.B., M.N., J.E.M.), Harvard Medical School, MA.,Department of Cardiology (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA.,Boston Children's Hospital and Department of Surgery (M.T.B., M.N., J.E.M.), Harvard Medical School, MA.,Department of Pediatrics (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA.,Division of Cardiac Surgery, Department of Surgery (M.T.B.), Harvard Medical School, MA.,Department of Genetics (M.T.B., J.H., S.M., A.T., J.G., J.G.S., C.E.S.), Harvard Medical School, MA
| | - Jason Homsy
- Department of Genetics (M.T.B., J.H., S.M., A.T., J.G., J.G.S., C.E.S.), Harvard Medical School, MA
| | - Meena Nathan
- Department of Cardiac Surgery (M.T.B., M.N., J.E.M.), Harvard Medical School, MA.,Boston Children's Hospital and Department of Surgery (M.T.B., M.N., J.E.M.), Harvard Medical School, MA
| | - Lynn A Sleeper
- Department of Cardiology (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA.,Department of Pediatrics (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA
| | - Sarah Morton
- Department of Newborn Medicine (S.M.), Harvard Medical School, MA.,Department of Genetics (M.T.B., J.H., S.M., A.T., J.G., J.G.S., C.E.S.), Harvard Medical School, MA
| | - Kathryn B Manheimer
- Mindich Child Health and Development Institute (K.B.M., B.D.G.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Angela Tai
- Department of Genetics (M.T.B., J.H., S.M., A.T., J.G., J.G.S., C.E.S.), Harvard Medical School, MA
| | - Joshua Gorham
- Department of Genetics (M.T.B., J.H., S.M., A.T., J.G., J.G.S., C.E.S.), Harvard Medical School, MA
| | - Matthew Lewis
- Departments of Pediatrics and Medicine (M.L., W.K.C.), New York-Presbyterian Hospital/Columbia University Medical Center
| | - Michael Swartz
- Department of Cardiac Surgery, University of Rochester, NY (M.S., G.M.A.)
| | - George M Alfieris
- Department of Cardiac Surgery, University of Rochester, NY (M.S., G.M.A.)
| | - Emile A Bacha
- Division of Cardiac, Thoracic, and Vascular Surgery (E.A.B.), New York-Presbyterian Hospital/Columbia University Medical Center
| | - Mohsen Karimi
- Division of Cardiac Surgery (M.K.), Yale University School of Medicine, New Haven, CT
| | - David Meyer
- Department of Pediatric Cardiothoracic Surgery (D.M.), Steven and Alexandra Cohen Children's Medical Center of New York, New Hyde Park
| | - Khanh Nguyen
- Pediatric Cardiac Surgery, Maria Fareri Children's Hospital, Valhalla, NY (K.N.)
| | | | - Angela Romano-Adesman
- Department of Cardiology (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA.,Department of Cardiology (A.R.-A.), Steven and Alexandra Cohen Children's Medical Center of New York, New Hyde Park
| | - George A Porter
- Department of Pediatrics, University of Rochester Medical Center, NY (G.A.P.)
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.)
| | - Wendy K Chung
- Departments of Pediatrics and Medicine (M.L., W.K.C.), New York-Presbyterian Hospital/Columbia University Medical Center
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (D.S.).,Roddenberry Stem Cell Center at Gladstone, San Francisco, CA (D.S.).,Departments of Pediatrics and Biochemistry and Biophysics, University of California, San Francisco (D.S.)
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD (J.R.K.)
| | | | - Richard Lifton
- Department of Genetics (R.L., M.B.), Yale University School of Medicine, New Haven, CT
| | - Amy E Roberts
- Department of Pediatrics (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA
| | - J William Gaynor
- Department of Pediatrics (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA.,Department of Pediatric Cardiac Surgery, The Children's Hospital of Philadelphia, PA (J.W.G.)
| | - Bruce D Gelb
- Mindich Child Health and Development Institute (K.B.M., B.D.G.), Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Genetics and Genomic Sciences (B.D.G.), Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Pediatrics (B.D.G.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Richard Kim
- Pediatric Cardiac Surgery, Children's Hospital of Los Angeles, CA (R.K.)
| | - Jonathan G Seidman
- Department of Genetics (M.T.B., J.H., S.M., A.T., J.G., J.G.S., C.E.S.), Harvard Medical School, MA
| | - Martina Brueckner
- Department of Genetics (R.L., M.B.), Yale University School of Medicine, New Haven, CT.,Department of Pediatrics (M.B.), Yale University School of Medicine, New Haven, CT
| | - John E Mayer
- Department of Cardiac Surgery (M.T.B., M.N., J.E.M.), Harvard Medical School, MA.,Boston Children's Hospital and Department of Surgery (M.T.B., M.N., J.E.M.), Harvard Medical School, MA
| | - Jane W Newburger
- Department of Cardiology (M.T.B., L.A.S., A.E.R., J.W.N.), Harvard Medical School, MA
| | - Christine E Seidman
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital (C.E.S.), Harvard Medical School, MA.,Department of Genetics (M.T.B., J.H., S.M., A.T., J.G., J.G.S., C.E.S.), Harvard Medical School, MA.,Howard Hughes Medical Institute, Chevy Chase, MD (C.E.S.)
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36
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Homans JF, de Reuver S, Heung T, Silversides CK, Oechslin EN, Houben ML, McDonald-McGinn DM, Kruyt MC, Castelein RM, Bassett AS. The role of 22q11.2 deletion syndrome in the relationship between congenital heart disease and scoliosis. Spine J 2020; 20:956-963. [PMID: 31958577 PMCID: PMC7246162 DOI: 10.1016/j.spinee.2020.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT For over four decades, clinicians and researchers have suggested a relationship between congenital heart disease (CHD) and scoliosis, attributed to either the disease itself or to the long-term effects of cardiac surgery on the immature thoracic cage. However, no study has yet accounted for 22q11.2 deletion syndrome (22q11.2DS), the second most common cause of CHD after Down syndrome. 22q11.2DS has a scoliosis risk of 50%, but within 22q11.2DS a previous report found no significant association between scoliosis and CHD. We, therefore, hypothesized that scoliosis within a CHD cohort would be related to an underlying 22q11.2 deletion. PURPOSE To determine the prevalence of scoliosis in CHD patients with and without 22q11.2DS. STUDY DESIGN/SETTING Cross-sectional. PATIENT SAMPLE A well-characterized existing database of 315 adults with CHD (primarily tetralogy of Fallot), with (n=86) and without (n=229) 22q11.2DS, matched by sex and CHD severity, and excluding other known syndromic diagnoses. We compared the scoliosis prevalence of patients with 22q11.2DS and CHD patients to the prevalence of scoliosis in a cohort of adults with 22q11.2DS without CHD based on medical records. OUTCOME MEASURES Presence of scoliosis (Cobb angle ≥10°). METHODS We systematically determined the presence of scoliosis in all included patients using chest radiographs, blind to genetic diagnosis. Besides 22q11.2DS, we analyzed other suspected risk factors for scoliosis using a regression model: thoracotomy before the age of 12 years, severe CHD type and sex. RESULTS The prevalence of scoliosis in adults with CHD and 22q11.2DS (n=46, 53.5%) was significantly greater than in those without 22q11.2DS (n=18, 7.9%, p<.0001). The presence of a 22q11.2 deletion (odds ratio [OR] 25.4, 95% confidence interval [95% CI] 11.2-57.4, p<.0001), a history of thoracotomy before the age of 12 years (OR 3.5, 95% CI 1.6-8.1, p=.0027) and most complex CHD class (OR 2.3, 95% CI 1.1-4.7, p=.0196), but not sex, were significant independent predictors of scoliosis. In the 22q11.2DS group, a right-sided aortic arch was associated with a left thoracic scoliotic curve (p=.036). CONCLUSIONS The prevalence of scoliosis in those with CHD but without a 22q11.2 deletion approximates that of the general population. However, in the CHD population with a 22q11.2 deletion, the prevalence of scoliosis approximates that of others with 22q11.2DS. The pediatric surgical approach and severity of CHD were weaker independent contributors as compared to the 22q11.2 deletion. The results support the importance of a genetic diagnosis of 22q11.2DS to the risk of developing scoliosis in individuals with CHD. The 22q11.2 deletion may represent a common etiopathogenetic pathway for both CHD and scoliosis, possibly involving early laterality mechanisms.
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Affiliation(s)
- Jelle F Homans
- Department of Orthopedic Surgery, University Medical Center Utrecht, P.O. Box 85500, 3508 Utrecht, the Netherlands
| | - Steven de Reuver
- Department of Orthopedic Surgery, University Medical Center Utrecht, P.O. Box 85500, 3508 Utrecht, the Netherlands
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada M5G 2N2; The Dalglish Family 22q Clinic for Adults, University Health Network, 200 Elizabeth St, Toronto, ON, Canada
| | - Candice K Silversides
- The Dalglish Family 22q Clinic for Adults, University Health Network, 200 Elizabeth St, Toronto, ON, Canada; Toronto Congenital Cardiac Centre for Adults, Peter Munk Cardiac Centre, 585 University Ave, Toronto, ON, Canada M5G 2N2; Division of Cardiology, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Erwin N Oechslin
- The Dalglish Family 22q Clinic for Adults, University Health Network, 200 Elizabeth St, Toronto, ON, Canada; Toronto Congenital Cardiac Centre for Adults, Peter Munk Cardiac Centre, 585 University Ave, Toronto, ON, Canada M5G 2N2; Division of Cardiology, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Michiel L Houben
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Donna M McDonald-McGinn
- Division of Human Genetics, 22q and You Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Moyo C Kruyt
- Department of Orthopedic Surgery, University Medical Center Utrecht, P.O. Box 85500, 3508 Utrecht, the Netherlands
| | - René M Castelein
- Department of Orthopedic Surgery, University Medical Center Utrecht, P.O. Box 85500, 3508 Utrecht, the Netherlands
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada M5G 2N2; The Dalglish Family 22q Clinic for Adults, University Health Network, 200 Elizabeth St, Toronto, ON, Canada; Toronto Congenital Cardiac Centre for Adults, Peter Munk Cardiac Centre, 585 University Ave, Toronto, ON, Canada M5G 2N2; Division of Cardiology, Department of Medicine, University Health Network, Toronto, ON, Canada; Toronto General Research Institute and Campbell Family Mental Health Research Institute, Toronto, ON, Canada.
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37
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van Mil S, Heung T, Malecki S, Van L, Chang J, Breetvelt E, Wald R, Oechslin E, Silversides C, Bassett AS. Impact of a 22q11.2 Microdeletion on Adult All-Cause Mortality in Tetralogy of Fallot Patients. Can J Cardiol 2020; 36:1091-1097. [PMID: 32348848 DOI: 10.1016/j.cjca.2020.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/08/2020] [Accepted: 04/20/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Because of the importance of identifying factors that affect late outcomes in the increasing population of those with tetralogy of Fallot (TOF), we aimed to determine the effect of a 22q11.2 microdeletion on adult mortality, while accounting for pulmonary atresia, known to be enriched in 22q11.2 deletion syndrome (22q11.2DS). METHODS We studied 612 individuals with TOF recruited as adults at a single centre, 80 (13.1%) with molecularly confirmed 22q11.2 deletions and 532 without 22q11.2DS, followed for a total of 5961.3 person-years. Using a case-control design, Cox proportional hazard regression and Kaplan-Meier curves, we evaluated the effect of a 22q11.2 deletion on mortality and survival. RESULTS All-cause mortality was 1.87% per person-year in the 22q11.2DS-TOF group and 0.80% in the other-TOF group. The presence of a 22q11.2 microdeletion was a significant predictor of adult mortality in TOF (hazard ratio, 5.00; P < 0.0001), after accounting for pulmonary atresia (hazard ratio, 2.71; P = 0.0106) and other factors. Overall, individuals with 22q11.2DS died on average 17.7 years earlier (P = 0.0055) than others with TOF, predominantly of cardiovascular causes, with proportionately more sudden cardiac deaths in those with 22q11.2DS-TOF (n = 5 [38.5%] vs n = 5 [11.9%], other-TOF; P = 0.0447). Kaplan-Meier curves showed reduced survival for those with 22q11.2DS (P < 0.0001); probability of survival to age 45 years, without pulmonary atresia, was 72% (22q11.2DS-TOF) and 98% (other-TOF). CONCLUSIONS The results suggest that the 22q11.2 deletion significantly contributes to premature mortality in adults with TOF, mediated only in part by greater anatomic complexity. The interpretation of late outcome data in TOF will likely benefit from further genetic subtyping.
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Affiliation(s)
- Spencer van Mil
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
| | - Sarah Malecki
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
| | - Lily Van
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Janis Chang
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
| | - Elemi Breetvelt
- Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rachel Wald
- Toronto Congenital Cardiac Centre for Adults, Division of Cardiology at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network; and University of Toronto, Toronto, Ontario, Canada
| | - Erwin Oechslin
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada; Toronto Congenital Cardiac Centre for Adults, Division of Cardiology at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network; and University of Toronto, Toronto, Ontario, Canada
| | - Candice Silversides
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada; Toronto Congenital Cardiac Centre for Adults, Division of Cardiology at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network; and University of Toronto, Toronto, Ontario, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Toronto Congenital Cardiac Centre for Adults, Division of Cardiology at the Peter Munk Cardiac Centre, Department of Medicine, University Health Network; and University of Toronto, Toronto, Ontario, Canada; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada.
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38
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Hosono K, Kawase K, Kurata K, Niimi Y, Saitsu H, Minoshima S, Ohnishi H, Yamamoto T, Hikoya A, Tachibana N, Fukao T, Yamamoto T, Hotta Y. A case of childhood glaucoma with a combined partial monosomy 6p25 and partial trisomy 18p11 due to an unbalanced translocation. Ophthalmic Genet 2020; 41:175-182. [PMID: 32223580 DOI: 10.1080/13816810.2020.1744019] [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] [Indexed: 02/01/2023]
Abstract
Background: Chromosomal deletion involving the 6p25 region results in a clinically recognizable syndrome characterized by anterior eye chamber anomalies with risk of glaucoma and non-ocular malformations (6p25 deletion syndrome). We report a newborn infant case of childhood glaucoma with a combination of partial monosomy 6p25 and partial trisomy 18p11 due to an unbalanced translocation.Materials and methods: The patient was a 0-year-old girl. Both eyes showed aniridia and left eye Peters anomaly with multiple malformations. To identify the chromosomal aberrations in the patient with clinically suspected 6p25 deletion syndrome, we performed cytogenetic analysis (G-banding and multicolor fluorescent in-situ hybridization) and array-based comparative genomic hybridization (array-CGH) analysis.Results: Cytogenetic analyses revealed a derivative chromosome 6 with its distal short arm replaced by an extra copy of the short arm of chromosome 18. Array-CGH analysis detected a 4.6-Mb deletion at 6pter to 6p25.1 and 8.9-Mb duplication at 18pter to 18p11.22. To determine the breakpoint of the unbalanced rearrangement at the single-base level, we performed a long-range PCR for amplifying the junctional fragment of the translocation breakpoint. By sequencing the junctional fragment, we defined the unbalanced translocation as g.chr6:pter_4594783delinschr18:pter_8911541.Conclusions: A phenotype corresponding to combined monosomy 6p25 and trisomy 18p11 presented as childhood glaucoma associated with non-acquired (congenital) ocular anomalies consist of aniridia and Peters anomaly and other systemic malformations. To the best of our knowledge, this is the first report which demonstrated the breakpoint sequence of an unbalanced translocation in a Japanese infant with childhood glaucoma.
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Affiliation(s)
- Katsuhiro Hosono
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuhide Kawase
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kentaro Kurata
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yusuke Niimi
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shinsei Minoshima
- Department of Photomedical Genomics, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Takahiro Yamamoto
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Akiko Hikoya
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Nobutaka Tachibana
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Toshiyuki Fukao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Tetsuya Yamamoto
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
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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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40
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Lalani SR. Other genomic disorders and congenital heart disease. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:107-115. [DOI: 10.1002/ajmg.c.31762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/09/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Seema R. Lalani
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston Texas
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41
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Genetics of Congenital Heart Disease. Biomolecules 2019; 9:biom9120879. [PMID: 31888141 PMCID: PMC6995556 DOI: 10.3390/biom9120879] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
Congenital heart disease (CHD) is one of the most common birth defects. Studies in animal models and humans have indicated a genetic etiology for CHD. About 400 genes have been implicated in CHD, encompassing transcription factors, cell signaling molecules, and structural proteins that are important for heart development. Recent studies have shown genes encoding chromatin modifiers, cilia related proteins, and cilia-transduced cell signaling pathways play important roles in CHD pathogenesis. Elucidating the genetic etiology of CHD will help improve diagnosis and the development of new therapies to improve patient outcomes.
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42
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Song X, Wang X, Ding L, He D, Sun J, Xi N, Yin Y, Peng H, Sun L. Identification of a novel heterozygous missense mutation of SEMA3E (c.1327G>A; p. Ala443Thr) in a labor induced fetus with CHARGE syndrome. Mol Genet Genomic Med 2019; 8:e1034. [PMID: 31691538 PMCID: PMC6978240 DOI: 10.1002/mgg3.1034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND CHARGE syndrome is a complex multisystem genetic disease. We aimed to find the potential gene mutation in the labor induced fetus with CHARGE syndrome. METHODS Genomic DNA was extracted from the fetal thigh muscle tissue and the peripheral blood of his parents. The resulting exomes were sequenced using whole exome sequencing (WES) followed by the selection of the candidate causative mutation genes. The deleteriousness of the identified variants was predicted. Analysis of multiple alignment of protein sequences and protein conserved domains was performed by online software. Finally, Sanger sequencing was applied for validation of the identified variants in the WES. RESULTS After sequencing and bioinformatics filtering, a heterozygous missense mutation of SEMA3E (c.1327G>A; p. Ala443Thr) was found in the fetus, while the mutation was absent in his parents. Genotyping results showed that the mutation cosegregated fully with definite CHARGE phenotypes between the fetus and his parents. This change was located in the Sema superfamily and highly conserved across different species. Sanger validation result was consistent with the WES analysis. CONCLUSION Our investigations suggested that the heterozygous missense mutation of SEMA3E (c.1327G>A; p. Ala443Thr) may be a potential causal variant in the fetus with CHARGE syndrome.
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Affiliation(s)
- Xiao Song
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Xueyan Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Li Ding
- Department of Radiology, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Dan He
- Department of Maternal and Child Health Management, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Jin Sun
- Department of Pharmacy, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Na Xi
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Yan Yin
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Hui Peng
- Department of Ultrasound, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
| | - Lingling Sun
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu, Sichuan, China
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43
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Mastromoro G, Capalbo A, Guido CA, Torres B, Fabbretti M, Traversa A, Giancotti A, Ventriglia F, Bernardini L, Spalice A, Pizzuti A. Small 7p22.3 microdeletion: Case report of Snx8 haploinsufficiency and neurological findings. Eur J Med Genet 2019; 63:103772. [PMID: 31568860 DOI: 10.1016/j.ejmg.2019.103772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/05/2019] [Accepted: 09/20/2019] [Indexed: 11/29/2022]
Abstract
Some cases of chromosome 7p22.3 deletions have been reported, but the genotype-phenotype correlation is still uncertain. Neurodevelopmental delay and heart anomalies have been recorded as the most recurrent defects. We describe the clinical features of a four-year-old male child with a 139 kb deletion at 7p22.3 involving SNX8 gene, inherited from a mosaic mother. The same deletion is also present in the fetus on the ongoing third pregnancy of the couple with normal fetal ultrasound assessment. The proband was prenatally diagnosed with left kidney agenesis. He does not show any congenital heart disease, but mild intellectual disability, learning and language delay, and severe behavioral problems related to the hyperactive-impulsive and inattentive area. These clinical features are also evident in other 7p22 deletions cases involving the SNX8 gene, supporting the role of this gene in neurodevelopment. Conversely, the revision of all published cases with small 7p22 deletions and the absence of heart malformations in the present family confirm that this region is involved in heart development, anyway did not confirm the role of SNX8 in cardiac phenotypes, either due to the reduced penetrance or the involvement of other candidate genes.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, Viale Regina Elena 324, Rome, Italy
| | - Anna Capalbo
- Medical Genetics Unit, IRCCS Mendel Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Cristiana Alessia Guido
- Department of Pediatrics, Division of Child Neurology, Policlinico Umberto I Hospital, Sapienza University of Rome, Viale Regina Elena 324, Rome, Italy
| | - Barbara Torres
- Medical Genetics Unit, IRCCS Mendel Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Maria Fabbretti
- Medical Genetics Unit, IRCCS Mendel Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Alice Traversa
- Medical Genetics Unit, IRCCS Mendel Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Antonella Giancotti
- Department of Obstetrics, Gynecology and Urologic Sciences, Policlinico Umberto I Hospital, Sapienza University of Rome, Viale Regina Elena 324, Rome, Italy
| | - Flavia Ventriglia
- Department of Pediatrics, Pediatric Cardiology, Policlinico Umberto I Hospital, Sapienza University of Rome, Viale Regina Elena 324, Rome, Italy
| | - Laura Bernardini
- Medical Genetics Unit, IRCCS Mendel Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Alberto Spalice
- Department of Pediatrics, Division of Child Neurology, Policlinico Umberto I Hospital, Sapienza University of Rome, Viale Regina Elena 324, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, Viale Regina Elena 324, Rome, Italy; Medical Genetics Unit, IRCCS Mendel Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy.
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44
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Liu Y, Chang X, Glessner J, Qu H, Tian L, Li D, Nguyen K, Sleiman PMA, Hakonarson H. Association of Rare Recurrent Copy Number Variants With Congenital Heart Defects Based on Next-Generation Sequencing Data From Family Trios. Front Genet 2019; 10:819. [PMID: 31552105 PMCID: PMC6746959 DOI: 10.3389/fgene.2019.00819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/07/2019] [Indexed: 01/17/2023] Open
Abstract
Congenital heart defects (CHDs) are a common birth defect, affecting approximately 1% of newborn children in the United States. As previously reported, a significant number of CHDs are potentially attributed to altered copy number variants (CNVs). However, as many genomic variants are rare, a large-scale CNV triad study is necessary to characterize the genetic architecture of CHD. We used whole-exome sequencing (WES) data generated by the Pediatric Cardiac Genomics Consortium (PCGC), including a discovery dataset of 2,103 individuals from 760 nuclear family trios and an independent replication set of 4,808 individuals from 1,712 trios. The candidate targets uncovered were further validated through different platforms, including the Omni single-nucleotide polymorphism (SNP) array chip in 1,860 individuals and the whole-genome sequencing (WGS) data in 33 trios. The genes harboring CNVs of interest were then investigated for expression alternations based on cardiac tissue RNA-Seq data. We identified multiple CNVs in the WES data that associated with specific sub-phenotypes of CHD in approximately 2,400 families, including 98 de novo CNV regions. We identified five CNV loci harboring LIMS1, GCC2, RANBP2, TTC3, and MAP3K7CL, respectively, where those genes are highly expressed in human heart and/or mouse embryo heart at 15 days. Five novel CNV loci were uncovered, demonstrating altered expression of the respective candidate genes involved. To our knowledge, this is the largest trio-based WES study of CHD and, in addition to uncovering novel CHD targets, presents an extensive resource with the potential to provide important insights to the architecture and impact of CNVs in CHD.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Xiao Chang
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Joseph Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Huiqi Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Lifeng Tian
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kenny Nguyen
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
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45
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Xie HM, Taylor DM, Zhang Z, McDonald-McGinn DM, Zackai EH, Stambolian D, Hakonarson H, Morrow BE, Emanuel BS, Goldmuntz E. Copy number variations in individuals with conotruncal heart defects reveal some shared developmental pathways irrespective of 22q11.2 deletion status. Birth Defects Res 2019; 111:888-905. [PMID: 31222980 DOI: 10.1002/bdr2.1534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/28/2019] [Accepted: 05/23/2019] [Indexed: 12/26/2022]
Abstract
Over 50% of patients with 22q11.2 deletion syndrome (DS) have a conotruncal or related cardiac defect (CTRD). We hypothesized that similar genetic variants, developmental pathways and biological functions, contribute to disease risk for CTRD in patients without a 22q11.2 deletion (ND-CTRD) and with a 22q11.2 deletion (DS-CTRD). To test this hypothesis, we performed rare CNV (rCNV)-based analyses on 630 ND-CTRD cases and 602 DS-CTRD cases with comparable cardiac lesions separately and jointly. First, we detected a collection of heart development related pathways from Gene Ontology and Mammalian Phenotype Ontology analysis. We then constructed gene regulation networks using unique genes collected from the rCNVs found in the ND-CTRD and DS-CTRD cohorts. These gene networks were clustered and their predicted functions were examined. We further investigated expression patterns of those unique genes using publicly available mouse embryo microarray expression data from single-cell embryos to fully developed hearts. By these bioinformatics approaches, we identified a commonly shared gene expression pattern in both the ND-CTRD and DS-CTRD cohorts. Computational analysis of gene functions characterized with this expression pattern revealed a collection of significantly enriched terms related to cardiovascular development. By our combined analysis of rCNVs in the ND-CTRD and DS-CTRD cohorts, a group of statistically significant shared pathways, biological functions, and gene expression patterns were identified that can be tested in future studies for their biological relevance.
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Affiliation(s)
- Hongbo M Xie
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Donna M McDonald-McGinn
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elaine H Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dwight Stambolian
- Department of Ophthalmology and Human Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- The Center for Applied Genomics, Department of Pediatrics, The Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bernice E Morrow
- Department of Genetics, Yeshiva University, Albert Einstein College of Medicine, Bronx, New York
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Cardiology, The Children's Hospital of Philadelphia, Department of Pediatrics, Philadelphia, Pennsylvania
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46
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Tessier A, Callier P, LeMeur N, Frebourg T, Sabourin JC, Patrier S. Postmortem Diagnosis of Heart-hand Syndrome Associated With a 7p22.1p22.3 Deletion in a 16-week-old Fetus. Pediatr Dev Pathol 2019; 22:146-151. [PMID: 30193563 DOI: 10.1177/1093526618799293] [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: 11/15/2022]
Abstract
We report a male fetus with a 6.8 Mb deletion on chromosome 7p22.1p22.3 at 16 weeks of gestation. The fetus presented a heart-hand syndrome with great artery malposition, bilateral radial ray deficiency, a single pelvic kidney, and growth retardation. This deletion involves a minimal deleted region for cardiac malformation and the RAC1 gene, previously described in limb anomalies in mice. This fetus is the third human case with limb defects and RAC1 deletion.
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Affiliation(s)
- Aude Tessier
- 1 Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée et Service de Génétique, CHU Charles Nicolle, Rouen, France.,2 Service d'anatomopathologie, CHU Charles Nicolle, Rouen, France
| | - Patrick Callier
- 3 Service de Cytogénétique, Pole Technique et Biologie, CHU Dijon, Dijon, France
| | - Nathalie LeMeur
- 1 Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée et Service de Génétique, CHU Charles Nicolle, Rouen, France
| | - Thierry Frebourg
- 1 Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée et Service de Génétique, CHU Charles Nicolle, Rouen, France
| | | | - Sophie Patrier
- 2 Service d'anatomopathologie, CHU Charles Nicolle, Rouen, France
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Copy number variation analysis in bicuspid aortic valve-related aortopathy identifies TBX20 as a contributing gene. Eur J Hum Genet 2019; 27:1033-1043. [PMID: 30820038 DOI: 10.1038/s41431-019-0364-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/08/2019] [Accepted: 02/02/2019] [Indexed: 12/26/2022] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect (CHD), affecting 1-2% of the population. BAV is associated with thoracic aortic aneurysms (TAAs). Deleterious copy number variations (CNVs) were found previously in up to 10% of CHD cases. This study aimed at unravelling the contribution of deleterious deletions or duplications in 95 unrelated BAV/TAA patients. Seven unique or rare CNVs were validated, harbouring protein-coding genes with a role in the cardiovascular system. Based on the presence of overlapping CNVs in patients with cardiovascular phenotypes in the DECIPHER database, the identification of similar CNVs in whole-exome sequencing data of 67 BAV/TAA patients and suggested topological domain involvement from Hi-C data, supportive evidence was obtained for two genes (DGCR6 and TBX20) of the seven initially validated CNVs. A rare variant burden analysis using next-generation sequencing data from 637 BAV/TAA patients was performed for these two candidate genes. This revealed a suggestive genetic role for TBX20 in BAV/TAA aetiology, further reinforced by segregation of a rare TBX20 variant with the phenotype within a BAV/TAA family. To conclude, our results do not confirm a significant contribution for deleterious CNVs in BAV/TAA as only one potentially pathogenic CNV (1.05%) was identified. We cannot exclude the possibility that BAV/TAA is occasionally attributed to causal CNVs though, or that certain CNVs act as genetic risk factors by creating a sensitised background for BAV/TAA. Finally, accumulative evidence for TBX20 involvement in BAV/TAA aetiology underlines the importance of this transcription factor in cardiovascular disease.
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48
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Johnsen JI, Dyberg C, Wickström M. Neuroblastoma-A Neural Crest Derived Embryonal Malignancy. Front Mol Neurosci 2019; 12:9. [PMID: 30760980 PMCID: PMC6361784 DOI: 10.3389/fnmol.2019.00009] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/11/2019] [Indexed: 12/14/2022] Open
Abstract
Neuroblastoma is a neural crest derived malignancy of the peripheral nervous system and is the most common and deadliest tumor of infancy. It is characterized by clinical heterogeneity with a disease spectrum ranging from spontaneous regression without any medical intervention to treatment resistant tumors with metastatic spread and poor patient survival. The events that lead to the development of neuroblastoma from the neural crest have not been fully elucidated. Here we discuss factors and processes within the neural crest that when dysregulated have the potential to be initiators or drivers of neuroblastoma development. A more precise biological understanding of neuroblastoma causes and cell of origin is highly warranted. This will give valuable information for the development of medicines that specifically target molecules within neuroblastoma cells and also give hint about the mechanisms behind treatment resistance that is frequently seen in neuroblastoma.
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Affiliation(s)
- John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet (KI), Stockholm, Sweden
| | - Cecilia Dyberg
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet (KI), Stockholm, Sweden
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet (KI), Stockholm, Sweden
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49
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Haploinsufficiency of vascular endothelial growth factor related signaling genes is associated with tetralogy of Fallot. Genet Med 2018; 21:1001-1007. [PMID: 30232381 PMCID: PMC6752294 DOI: 10.1038/s41436-018-0260-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/26/2018] [Indexed: 12/18/2022] Open
Abstract
Purpose To determine disease-associated single-gene variants in conotruncal defects, particularly tetralogy of Fallot (TOF). Methods We analyzed for rare loss-of-function and deleterious variants in FLT4 (VEGFR3) and other genes in the vascular endothelial growth factor (VEGF) pathway, as part of a genome sequencing study involving 175 adults with TOF from a single site. Results We identified nine (5.1%) probands with novel FLT4 variants: seven loss-of-function, including an 8-kb deletion, and two predicted damaging. In ten other probands we found likely disruptive variants in VEGF-related genes: KDR (VEGFR2; two stopgain and two nonsynonymous variants), VEGFA, FGD5, BCAR1, IQGAP1, FOXO1, and PRDM1. Detection of VEGF-related variants (19/175, 10.9%) was associated with an increased prevalence of absent pulmonary valve (26.3% vs. 3.4%, p < 0.0001) and right aortic arch (52.6% vs. 29.1%, p = 0.029). Extracardiac anomalies were rare. In an attempt to replicate findings, we identified three loss-of-function or damaging variants in FLT4, KDR, and IQGAP1 in ten independent families with TOF. Conclusion Loss-of-function variants in FLT4 and KDR contribute substantially to the genetic basis of TOF. The findings support dysregulated VEGF signaling as a novel mechanism contributing to the pathogenesis of TOF.
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50
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Song T, Wan S, Li Y, Xu Y, Dang Y, Zheng Y, Li C, Zheng J, Chen B, Zhang J. Detection of copy number variants using chromosomal microarray analysis for the prenatal diagnosis of congenital heart defects with normal karyotype. J Clin Lab Anal 2018; 33:e22630. [PMID: 30047171 DOI: 10.1002/jcla.22630] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/04/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND With the increasing availability of chromosomal microarray analysis (CMA) for congenital heart defect (CHD), genetic testing now faces new challenges due to results with uncertain clinical impact. Studies are needed to better define the penetrance of genetic variants. The aim of the study was to examine the association between CMA and CHDs in fetuses with normal karyotype. METHODS This was a retrospective study of 190 fetuses with normal karyotype that underwent CMA after a diagnosis of CHD by fetal ultrasound. Invasive prenatal diagnosis was performed between January 2015 and December 2016 at the first affiliated hospital of Air Force Medical University. RESULTS Chromosomal microarray analysis detected pathogenic copy number variants (pCNVs) in 13/190 (6.84%) fetuses, likely pCNVs in 5/190 (2.63%), and variants of unknown significance (VOUS) in 14/190 (7.37%). Among those with pCNVs, none (0%) yielded a normal live birth. Among those with likely pCNVs, 2/5 (40.0%) yielded a live birth. Among the fetuses with VOUS, 10/14 (71.5%) yielded a live birth. CONCLUSION These results highlight the usefulness of CMA for prenatal genetic diagnosis of fetuses with CHDs and normal karyotype. In fetuses with CHD, the application of CMA could increase the detection rate of pCNVs causing CHDs. In this study, some VOUS were likely pathogenic, but additional studies are necessary to confirm these findings.
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Affiliation(s)
- Tingting Song
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Shanning Wan
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Yu Li
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Ying Xu
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Yinghui Dang
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Yunyun Zheng
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Chunyan Li
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Jiao Zheng
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Biliang Chen
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
| | - Jianfang Zhang
- Department of Obstetrics and Gynecology, the first affiliated hospital of Air Force Medical University, Xi'an, China
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