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Alfayyadh MM, Maksemous N, Sutherland HG, Lea RA, Griffiths LR. Unravelling the Genetic Landscape of Hemiplegic Migraine: Exploring Innovative Strategies and Emerging Approaches. Genes (Basel) 2024; 15:443. [PMID: 38674378 PMCID: PMC11049430 DOI: 10.3390/genes15040443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Migraine is a severe, debilitating neurovascular disorder. Hemiplegic migraine (HM) is a rare and debilitating neurological condition with a strong genetic basis. Sequencing technologies have improved the diagnosis and our understanding of the molecular pathophysiology of HM. Linkage analysis and sequencing studies in HM families have identified pathogenic variants in ion channels and related genes, including CACNA1A, ATP1A2, and SCN1A, that cause HM. However, approximately 75% of HM patients are negative for these mutations, indicating there are other genes involved in disease causation. In this review, we explored our current understanding of the genetics of HM. The evidence presented herein summarises the current knowledge of the genetics of HM, which can be expanded further to explain the remaining heritability of this debilitating condition. Innovative bioinformatics and computational strategies to cover the entire genetic spectrum of HM are also discussed in this review.
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Affiliation(s)
| | | | | | | | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia; (M.M.A.); (N.M.); (H.G.S.); (R.A.L.)
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2
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Liu YH, Luo C, Golding SG, Ioffe JB, Zhou XM. Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data. Nat Commun 2024; 15:2447. [PMID: 38503752 PMCID: PMC10951360 DOI: 10.1038/s41467-024-46614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
Long-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational efficiency and lower coverage requirements, are prominent. Alternative approaches, relying solely on available reads for de novo genome assembly and employing assembly-based tools for SV detection via comparison to a reference genome, demand significantly more computational resources. However, the lack of comprehensive benchmarking constrains our comprehension and hampers further algorithm development. Here we systematically compare 14 read alignment-based SV calling methods (including 4 deep learning-based methods and 1 hybrid method), and 4 assembly-based SV calling methods, alongside 4 upstream aligners and 7 assemblers. Assembly-based tools excel in detecting large SVs, especially insertions, and exhibit robustness to evaluation parameter changes and coverage fluctuations. Conversely, alignment-based tools demonstrate superior genotyping accuracy at low sequencing coverage (5-10×) and excel in detecting complex SVs, like translocations, inversions, and duplications. Our evaluation provides performance insights, highlighting the absence of a universally superior tool. We furnish guidelines across 31 criteria combinations, aiding users in selecting the most suitable tools for diverse scenarios and offering directions for further method development.
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Affiliation(s)
- Yichen Henry Liu
- Department of Computer Science, Vanderbilt University, 37235, Nashville, TN, USA
| | - Can Luo
- Department of Biomedical Engineering, Vanderbilt University, 37235, Nashville, TN, USA
| | - Staunton G Golding
- Department of Biomedical Engineering, Vanderbilt University, 37235, Nashville, TN, USA
| | - Jacob B Ioffe
- Department of Computer Science, Vanderbilt University, 37235, Nashville, TN, USA
| | - Xin Maizie Zhou
- Department of Computer Science, Vanderbilt University, 37235, Nashville, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, 37235, Nashville, TN, USA.
- Data Science Institute, Vanderbilt University, 37235, Nashville, TN, USA.
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3
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Maddhesiya J, Mohapatra B. Understanding the Genetic and Non-genetic Interconnections in the Aetiology of Isolated Congenital Heart Disease: An Updated Review: Part 1. Curr Cardiol Rep 2024; 26:147-165. [PMID: 38546930 DOI: 10.1007/s11886-024-02022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE OF REVIEW Congenital heart disease (CHD) is the most frequently occurring birth defect. Majority of the earlier reviews focussed on the association of genetic factors with CHD. A few epidemiological studies provide convincing evidence for environmental factors in the causation of CHD. Although the multifactorial theory of gene-environment interaction is the prevailing explanation, explicit understanding of the biological mechanism(s) involved, remains obscure. Nonetheless, integration of all the information into one platform would enable us to better understand the collective risk implicated in CHD development. RECENT FINDINGS Great strides in novel genomic technologies namely, massive parallel sequencing, whole exome sequencing, multiomics studies supported by system-biology have greatly improved our understanding of the aetiology of CHD. Molecular genetic studies reveal that cardiac specific gene variants in transcription factors or signalling molecules, or structural proteins could cause CHD. Additionally, non-hereditary contributors such as exposure to teratogens, maternal nutrition, parental age and lifestyle factors also contribute to induce CHD. Moreover, DNA methylation and non-coding RNA are also correlated with CHD. Here, we inform that a complex combination of genetic, environmental and epigenetic factors interact to interfere with morphogenetic processes of cardiac development leading to CHD. It is important, not only to identify individual genetic and non-inherited risk factors but also to recognize which factors interact mutually, causing cardiac defects.
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Affiliation(s)
- Jyoti Maddhesiya
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi, 221005, India.
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4
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Brown C, Stefaniuk-Szmukier M, Decloedt A, Beijerink N, Hamilton NA, Velie BD. Congenital heart defects in Arabian horses and the prospects of genetic testing: A review. Equine Vet J 2024. [PMID: 38272847 DOI: 10.1111/evj.14062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
Congenital heart defects (CHDs) can have profound and potentially life-threatening consequences on horses' health and performance capability. While CHDs are rare in the general horse population, the Arabian breed is disproportionately overrepresented and thus is widely suspected to be genetically predisposed. This review discusses the most common CHDs in Arabian horses, including ventricular septal defect (VSD), tetralogy of Fallot (TOF), patent duct arteriosus (PDA), tricuspid valve atresia (TVA) and atrial septal defect (ASD). This review also explores how future research into the genetic factors that likely underpin many CHDs can revolutionise the way these disorders are managed in Arabian horses.
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Affiliation(s)
- Caitlin Brown
- Equine Genetics and Genomics Group, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Monika Stefaniuk-Szmukier
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Annelies Decloedt
- Equine Cardioteam Ghent, Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Niek Beijerink
- Veterinaire Specialisten Vught, Vught, The Netherlands
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Natasha A Hamilton
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Brandon D Velie
- Equine Genetics and Genomics Group, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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5
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Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD, Poterba T, Wilson MW, Tarasova Y, Phu W, Grant R, Yohannes MT, Koenig Z, Farjoun Y, Banks E, Donnelly S, Gabriel S, Gupta N, Ferriera S, Tolonen C, Novod S, Bergelson L, Roazen D, Ruano-Rubio V, Covarrubias M, Llanwarne C, Petrillo N, Wade G, Jeandet T, Munshi R, Tibbetts K, O'Donnell-Luria A, Solomonson M, Seed C, Martin AR, Talkowski ME, Rehm HL, Daly MJ, Tiao G, Neale BM, MacArthur DG, Karczewski KJ. A genomic mutational constraint map using variation in 76,156 human genomes. Nature 2024; 625:92-100. [PMID: 38057664 DOI: 10.1038/s41586-023-06045-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/03/2023] [Indexed: 12/08/2023]
Abstract
The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders1-4, but attempts to assess constraint for non-protein-coding regions have proved more difficult. Here we aggregate, process and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD)-the largest public open-access human genome allele frequency reference dataset-and use it to build a genomic constraint map for the whole genome (genomic non-coding constraint of haploinsufficient variation (Gnocchi)). We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation. As expected, the average constraint for protein-coding sequences is stronger than that for non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants that are implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, which in turn suggests that non-coding constraint can aid the identification of constrained genes that are as yet unrecognized by current gene constraint metrics. We demonstrate that this genome-wide constraint map improves the identification and interpretation of functional human genetic variation.
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Affiliation(s)
- Siwei Chen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
| | - Laurent C Francioli
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Julia K Goodrich
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Masahiro Kanai
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Qingbo Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Jessica Alföldi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas A Watts
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher Vittal
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy Poterba
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael W Wilson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Yekaterina Tarasova
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William Phu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Riley Grant
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mary T Yohannes
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zan Koenig
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yossi Farjoun
- Richards Lab, Lady Davis Institute, Montreal, Quebec, Canada
| | - Eric Banks
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Stacey Gabriel
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven Ferriera
- Broad Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sam Novod
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Louis Bergelson
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Roazen
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Miguel Covarrubias
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nikelle Petrillo
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gordon Wade
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault Jeandet
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruchi Munshi
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Tibbetts
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Matthew Solomonson
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Cotton Seed
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Grace Tiao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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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 Pediatr Congenit Heart Dis 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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Horii Y, Kuroda Y, Saito Y, Enomoto Y, Naruto T, Kurosawa K. A CAMK2B variant associated with tetralogy of Fallot, developmental delay, and growth retardation. Eur J Med Genet 2023; 66:104845. [PMID: 37734707 DOI: 10.1016/j.ejmg.2023.104845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
CAMK2B encodes the beta-subunit of calcium/calmodulin-dependent protein kinase II (CAMKII), which is expressed mainly in the brain. Variants of CAMK2A and CAMK2B cause neurodevelopmental disorders, and CAMK2B alterations have been described in at least 14 patients with intellectual disability and developmental delay. Here, we describe a novel CAMK2B variant in a patient with tetralogy of Fallot (TOF), developmental delay, and growth retardation. The patient was a 2-year-old female. She was delivered at 36 weeks 6 days gestational age by caesarean section due to non-reassuring fetal status, with birth weight of 1680 g (-2.0 SD), birth length of 43.5 cm (-1.5 SD), and occipital-frontal head circumference (OFC) of 29.4 cm (-1.7 SD). Growth retardation, microcephaly, developmental delay, tetralogy of Fallot, and dysmorphic features were present. The patient controlled her head position at four months, rolled at six months, sat at 13 months, crawled at 18 months, and walked with support at 21 months. She began speaking words at 2 years old. Her dysmorphic features included a wide face, broad forehead, puffy eyelids, broad nasal base, broad and prominent philtrum, pointed chin, full cheeks, and prominent ears. A de novo missense CAMK2B variant (NM_172079.2:c.895A > G (p.Lys299Glu) NC_000007.14:g.44241708T > C (hg38)) was identified by proband exome sequencing and confirmed by Sanger sequencing. The variant was located at an autoregulatory segment and highly conserved among species. This patient displayed many of the physical features of CAMK2B-related neurodevelopmental disorder (NDD), but the TOF present in the current case is not a feature of patients with the NDD. Since a de novo CAMK2B (p.Leu443Val) variant has previously been found in a cohort of TOF, we conclude that CAMK2B variants may be associated with this specific cardiac defect.
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Affiliation(s)
- Yuji Horii
- Division of Medical Genetics, Kanagawa Children's Medical Center, Japan
| | - Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Japan.
| | - Yoko Saito
- Division of Medical Genetics, Kanagawa Children's Medical Center, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Japan.
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8
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Chan CH, Lam YY, Wong N, Geng L, Zhang J, Ahola V, Zare A, Li RA, Lanner F, Keung W, Cheung YF. Abnormal developmental trajectory and vulnerability to cardiac arrhythmias in tetralogy of Fallot with DiGeorge syndrome. Commun Biol 2023; 6:969. [PMID: 37740059 PMCID: PMC10516936 DOI: 10.1038/s42003-023-05344-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. Ventricular dysfunction and cardiac arrhythmias are well-documented complications in patients with repaired TOF. Whether intrinsic abnormalities exist in TOF cardiomyocytes is unknown. We establish human induced pluripotent stem cells (hiPSCs) from TOF patients with and without DiGeorge (DG) syndrome, the latter being the most commonly associated syndromal association of TOF. TOF-DG hiPSC-derived cardiomyocytes (hiPSC-CMs) show impaired ventricular specification, downregulated cardiac gene expression and upregulated neural gene expression. Transcriptomic profiling of the in vitro cardiac progenitors reveals early bifurcation, as marked by ectopic RGS13 expression, in the trajectory of TOF-DG-hiPSC cardiac differentiation. Functional assessments further reveal increased arrhythmogenicity in TOF-DG-hiPSC-CMs. These findings are found only in the TOF-DG but not TOF-with no DG (ND) patient-derived hiPSC-CMs and cardiac progenitors (CPs), which have implications on the worse clinical outcomes of TOF-DG patients.
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Affiliation(s)
- Chun-Ho Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yin-Yu Lam
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Nicodemus Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lin Geng
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jilin Zhang
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
| | - Virpi Ahola
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
| | - Aman Zare
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
| | - Ronald Adolphus Li
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, The University of Hong Kong, Hong Kong, China
| | - Fredrik Lanner
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavagen 9, 17165, Stockholm, Sweden
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden
| | - Wendy Keung
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, The University of Hong Kong, Hong Kong, China
| | - Yiu-Fai Cheung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Ming Wai Lau Centre for Reparative Medicine, Hong Kong node, Karolinska Institutet, Units 608-613 Building 15 Science Park, Hong Kong, China.
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, The University of Hong Kong, Hong Kong, China.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Yu X, Tao Y, Liu X, Yu F, Jiang C, Xiao Y, Zhang H, He Y, Ye L, Wang Y, Zhou C, Wang J, Jiang Z, Hong H. The implication of chromosomal abnormalities in the surgical outcomes of Chinese pediatric patients with congenital heart disease. Front Cardiovasc Med 2023; 10:1164577. [PMID: 37293289 PMCID: PMC10244782 DOI: 10.3389/fcvm.2023.1164577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/05/2023] [Indexed: 06/10/2023] Open
Abstract
Background Copy number variations (CNVs) have been shown to be overrepresented in children with congenital heart disease (CHD). Genetic evaluation of CHD is currently underperformed in China. We sought to determine the occurrence of CNVs in CNV regions with disease-causing potential among a large cohort of Chinese pediatric CHD patients and investigate whether these CNVs could be the important critical modifiers of surgical intervention. Methods CNVs screenings were performed in 1,762 Chinese children who underwent at least one cardiac surgery. CNV status at over 200 CNV locus with disease-causing potential was analyzed with a high-throughput ligation-dependent probe amplification (HLPA) assay. Results We found 378 out of 1,762 samples (21.45%) to have at least one CNV and 2.38% of them were carrying multiple CNVs. The detection rates of ppCNVs (pathogenic and likely pathogenic CNVs) were 9.19% (162/1,762), significantly higher than that of the healthy Han Chinese individuals from The Database of Genomic Variants archive (9.19% vs. 3.63%; P = 0.0012). CHD cases with ppCNVs had a significantly higher proportion of complex surgeries compared to CHD patients with no ppCNVs (62.35% vs. 37.63%, P < 0.001). Duration of cardiopulmonary bypass and aortic cross clamp procedures were significantly longer in CHD cases with ppCNVs (all P < 0.05), while no group differences were identified for complications of surgery and one-month mortality after surgery. The detection rate of ppCNVs in the atrioventricular septal defect (AVSD) subgroup was significantly higher than that in other subgroups (23.10% vs. 9.70%, P = 0.002). Conclusions CNV burden is an important contributor to Chinese children with CHD. Our study demonstrated the robustness and diagnostic efficiency of HLPA method in the genetic screening of CNVs in CHD patients.
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Affiliation(s)
- Xiafeng Yu
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu Tao
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Xu Liu
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Feng Yu
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Chuan Jiang
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yingying Xiao
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Haibo Zhang
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yongrui He
- Institute of Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lincai Ye
- Institute of Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Wang
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Chunxia Zhou
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhengwen Jiang
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Haifa Hong
- Institute of Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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11
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Hu H, Geng Z, Zhang S, Xu Y, Wang Q, Chen S, Zhang B, Sun K, Lu Y. Rare copy number variation analysis identifies disease-related variants in atrioventricular septal defect patients. Front Genet 2023; 14:1075349. [PMID: 36816019 PMCID: PMC9936062 DOI: 10.3389/fgene.2023.1075349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Atrioventricular septal defect (AVSD) is a deleterious subtype of congenital heart diseases (CHD) characterized by atrioventricular canal defect. The pathogenic genetic changes of AVSD remain elusive, particularly for copy number variation (CNV), a large segment variation of the genome, which is one of the major forms of genetic variants resulting in congenital heart diseases. In the present study, we recruited 150 AVSD cases and 100 healthy subjects as controls for whole exome sequencing (WES). We identified total 4255 rare CNVs using exon Hidden Markov model (XHMM) and screened rare CNVs by eliminating common CNVs based on controls and Database of Genomic Variants (DGV). Each patient contained at least 9 CNVs, and the CNV burden was prominently presented in chromosomes 19,22,21&16. Small CNVs (<500 kb) were frequently observed. By leveraging gene-based burden test, we further identified 20 candidate AVSD-risk genes. Among them, DYRK1A, OBSCN and TTN were presented in the core disease network of CHD and highly and dynamically expressed in the heart during the development, which indicated they possessed the high potency to be AVSD-susceptible genes. These findings not only provided a roadmap for finally unveiling the genetic cause of AVSD, but also provided more resources and proofs for clinical genetics.
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Affiliation(s)
- Huan Hu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuejuan Xu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qingjie Wang
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bing Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
| | - Kun Sun
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
| | - Yanan Lu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
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12
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Lansdon LA, Dickinson A, Arlis S, Liu H, Hlas A, Hahn A, Bonde G, Long A, Standley J, Tyryshkina A, Wehby G, Lee NR, Daack-Hirsch S, Mohlke K, Girirajan S, Darbro BW, Cornell RA, Houston DW, Murray JC, Manak JR. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes. Am J Hum Genet 2023; 110:71-91. [PMID: 36493769 PMCID: PMC9892779 DOI: 10.1016/j.ajhg.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology, University of Missouri - Kansas City School of Medicine, Kansas City, MO 64108, USA
| | | | - Sydney Arlis
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Huan Liu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Arman Hlas
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Alyssa Hahn
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Greg Bonde
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Abby Long
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | | | - George Wehby
- College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Nanette R Lee
- Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | | | - Karen Mohlke
- University of North Carolina, Chapel Hill, NC 27514, USA
| | | | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Robert A Cornell
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Douglas W Houston
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - J Robert Manak
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA.
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13
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Cai R, Tan Y, Wang M, Yu H, Wang J, Ren Z, Dong Z, He Y, Li Z, Lin L, Gu Y. Detection of Novel Pathogenic Variants in Two Families with Recurrent Fetal Congenital Heart Defects. Pharmgenomics Pers Med 2023; 16:173-181. [PMID: 36923242 PMCID: PMC10008912 DOI: 10.2147/pgpm.s394120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/17/2023] [Indexed: 03/10/2023] Open
Abstract
Background Congenital heart disease (CHD) is the most common birth defect with strong genetic heterogeneity. To date, about 400 genes have been linked to CHD, including cell signaling molecules, transcription factors, and structural proteins that are important for heart development. Genetic analysis of CHD cases is crucial for clinical management and etiological analysis. Methods Whole-exome sequencing (WES) was performed to identify the genetic variants in two independent CHD cases with DNA samples from fetuses and their parents, followed by the exclusion of aneuploidy and large copy number variations (CNVs). The WES results were verified by Sanger sequencing. Results In family A, a compound heterozygous variation in PLD1 gene consisting of c.1132dupA (p.I378fs) and c.1171C>T (p.R391C) was identified in the fetus. The two variants were inherited from the father (c.1132dupA) and the mother (c.1171C>T), respectively. In family B, a hemizygous variant ZIC3: c.861delG (p.G289Afs*119) was identified in the fetus, which was inherited from the heterozygous mother. We further confirmed that these variants PLD1: c.1132dupA and ZIC3: c.861delG were novel. Conclusion The findings in our study identified novel variants to the mutation spectrum of CHD and provided reliable evidence for the recurrent risk and reproductive care options to the affected families. Our study also demonstrates that WES has considerable prospects of clinical application in prenatal diagnosis.
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Affiliation(s)
- Rongqin Cai
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Ya Tan
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Mingming Wang
- Be Creative Lab (Beijing) Co. Ltd, Beijing, 101111, People's Republic of China
| | - Huijun Yu
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Jing Wang
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Zhuo Ren
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Zhe Dong
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Yiwen He
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Zhi Li
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Li Lin
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China
| | - Ying Gu
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, 102206, People's Republic of China.,Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
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14
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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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15
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Bao B, Hu H, Chen L, Lu S, Tang Q, Liang Z. SNP and DNA methylation analyses of a monozygotic twins discordant for complete endocardial cushion defect: a case report. Am J Transl Res 2022; 14:8271-8278. [PMID: 36505317 PMCID: PMC9730093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 12/15/2022]
Abstract
The exact cause of complete endocardial cushion defect (ECD) is still unknown. This report describes a unique pair of monozygotic twins (MZ twins) discordant for ECD. The chromosome karyotyping analysis revealed normal karyotype of 46, XY, 16qh+ and mat in both MZ twins. A genome-wide analysis of DNA using the Affymetrix SNP 6.0 revealed identical genotyping of single nucleotide polymorphisms (SNPs) and copy number variations (CNVs). An extensive methylation assay was carried out by NimbleGen 3 × 720 K CpG Island Plus RefSeq Promoter Arrays to analyze the potential epigenetic differences. The DNA methylation profiles of the affected twin seemed increased compared with that of the unaffected twin. However, further validation of Notch1 promoter hypermethylation and six top-ranked differentially methylated CpG sites by sodium bisulfate modification and methylation-specific PCR, failed to reveal consistent methylation differences between the twins. Other relevant factors, such as heritability and penetrance of the condition that place the MZ twins near to a threshold for ECD or variations in local epigenetic events in the twins' heart tissues, are probably responsible for the phenotypic discordance.
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Affiliation(s)
- Bihui Bao
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Hua Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital (Xinqiao Hospital), Army Medical UniversityChongqing 400037, China
| | - Limei Chen
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Shiyong Lu
- Department of Obstetrics and Gynecology, Qingbaijiang Women’s and Children’s Hospital (Maternal and Child Health Hospital), West China Second University Hospital, Sichuan UniversityChengdu 610300, Sichuan, China
| | - Qifeng Tang
- Department of Anesthesiology, Shanghai Hechuan-Rhine TCM HospitalShanghai 201103, China
| | - Zhiqing Liang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital (Southwest Hospital), Army Medical UniversityChongqing 400038, China
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16
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Chen Z, Chen HX, Hou HT, Yin XY, Yang Q, He GW. Pathophysiological Role of Variants of the Promoter Region of CITED2 Gene in Sporadic Tetralogy of Fallot Patients with Cellular Function Verification. Biomolecules 2022; 12:1644. [PMID: 36358994 PMCID: PMC9687598 DOI: 10.3390/biom12111644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2023] Open
Abstract
Tetralogy of Fallot (TOF) is a common congenital heart malformation. Genetic variants in the CITED2 coding region are known to be significantly associated with cardiac malformation, but the role of variants in the CITED2 promoter region in the development of TOF remains unclear. In this study, we investigated CITED2 promoter variants in the DNA of 605 subjects, including 312 TOF patients and 293 unrelated healthy controls, by Sanger sequencing. We identified nine CITED2 gene promoter variants (including one novel heterozygous variant). Six were found only in patients with TOF and none in the control group. The transcriptional activity of the CITED2 gene promoter in mouse cardiomyocyte (HL-1) cells was significantly altered by the six variants (p < 0.05). The results of the electrophoretic mobility change assay and JASPAR database analysis showed that these variants generated or destroyed a series of possible transcription factor binding sites, resulting in changes in the CITED2 protein expression. We conclude that CITED2 promoter variants in TOF patients affect transcriptional activity and may be involved in the occurrence and progression of TOF. These findings may provide new insights into molecular pathogenesis and potential therapeutic insights in patients with TOF.
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Affiliation(s)
- Zhuo Chen
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Hai-Tao Hou
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Xiu-Yun Yin
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
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17
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Abstract
The application of next-generation sequencing to study congenital heart disease (CHD) is increasingly providing new insights into the causes and mechanisms of this prevalent birth anomaly. Whole-exome sequencing analysis identifies damaging gene variants altering single or contiguous nucleotides that are assigned pathogenicity based on statistical analyses of families and cohorts with CHD, high expression in the developing heart and depletion of damaging protein-coding variants in the general population. Gene classes fulfilling these criteria are enriched in patients with CHD and extracardiac abnormalities, evidencing shared pathways in organogenesis. Developmental single-cell transcriptomic data demonstrate the expression of CHD-associated genes in particular cell lineages, and emerging insights indicate that genetic variants perturb multicellular interactions that are crucial for cardiogenesis. Whole-genome sequencing analyses extend these observations, identifying non-coding variants that influence the expression of genes associated with CHD and contribute to the estimated ~55% of unexplained cases of CHD. These approaches combined with the assessment of common and mosaic genetic variants have provided a more complete knowledge of the causes and mechanisms of CHD. Such advances provide knowledge to inform the clinical care of patients with CHD or other birth defects and deepen our understanding of the complexity of human development. In this Review, we highlight known and candidate CHD-associated human genes and discuss how the integration of advances in developmental biology research can provide new insights into the genetic contributions to CHD.
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Affiliation(s)
- Sarah U. Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | - Daniel Quiat
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA.,These authors contributed equally: Sarah U. Morton, Daniel Quiat
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard University, Boston, MA, USA.,
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19
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Tang CSM, Mononen M, Lam WY, Jin SC, Zhuang X, Garcia-Barcelo MM, Lin Q, Yang Y, Sahara M, Eroglu E, Chien KR, Hong H, Tam PK, Gruber PJ. Sequencing of a Chinese tetralogy of fallot cohort reveals clustering mutations in myogenic heart progenitors. JCI Insight 2021; 7:152198. [PMID: 34905512 PMCID: PMC8855809 DOI: 10.1172/jci.insight.152198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic heart defect, yet the underlying genetic mechanisms remain poorly understood. Here, we performed whole-genome sequencing analysis on 146 nonsyndromic TOF parent-offspring trios of Chinese ethnicity. Comparison of de novo variants and recessive genotypes of this data set with data from a European cohort identified both overlapping and potentially novel gene loci and revealed differential functional enrichment between cohorts. To assess the impact of these mutations on early cardiac development, we integrated single-cell and spatial transcriptomics of early human heart development with our genetic findings. We discovered that the candidate gene expression was enriched in the myogenic progenitors of the cardiac outflow tract. Moreover, subsets of the candidate genes were found in specific gene coexpression modules along the cardiomyocyte differentiation trajectory. These integrative functional analyses help dissect the pathogenesis of TOF, revealing cellular hotspots in early heart development resulting in cardiac malformations.
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Affiliation(s)
- Clara Sze Man Tang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Mimmi Mononen
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Wai-Yee Lam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, United States of America
| | - Xuehan Zhuang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Qiongfen Lin
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yujia Yang
- Department of Surgery, Yale University School of Medicine, New Haven, United States of America
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Elif Eroglu
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Haifa Hong
- Department of Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai, China
| | - Paul Kh Tam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Peter J Gruber
- Yale University School of Medicine, New Haven, United States of America
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20
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Matos-Nieves A, Manivannan S, Majumdar U, McBride KL, White P, Garg V. A Multi-Omics Approach Using a Mouse Model of Cardiac Malformations for Prioritization of Human Congenital Heart Disease Contributing Genes. Front Cardiovasc Med 2021; 8:683074. [PMID: 34504875 PMCID: PMC8421733 DOI: 10.3389/fcvm.2021.683074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023] Open
Abstract
Congenital heart disease (CHD) is the most common type of birth defect, affecting ~1% of all live births. Malformations of the cardiac outflow tract (OFT) account for ~30% of all CHD and include a range of CHDs from bicuspid aortic valve (BAV) to tetralogy of Fallot (TOF). We hypothesized that transcriptomic profiling of a mouse model of CHD would highlight disease-contributing genes implicated in congenital cardiac malformations in humans. To test this hypothesis, we utilized global transcriptional profiling differences from a mouse model of OFT malformations to prioritize damaging, de novo variants identified from exome sequencing datasets from published cohorts of CHD patients. Notch1+/−; Nos3−/− mice display a spectrum of cardiac OFT malformations ranging from BAV, semilunar valve (SLV) stenosis to TOF. Global transcriptional profiling of the E13.5 Notch1+/−; Nos3−/− mutant mouse OFTs and wildtype controls was performed by RNA sequencing (RNA-Seq). Analysis of the RNA-Seq dataset demonstrated genes belonging to the Hif1α, Tgf-β, Hippo, and Wnt signaling pathways were differentially expressed in the mutant OFT. Mouse to human comparative analysis was then performed to determine if patients with TOF and SLV stenosis display an increased burden of damaging, genetic variants in gene homologs that were dysregulated in Notch1+/−; Nos3−/− OFT. We found an enrichment of de novo variants in the TOF population among the 1,352 significantly differentially expressed genes in Notch1+/−; Nos3−/− mouse OFT but not the SLV population. This association was not significant when comparing only highly expressed genes in the murine OFT to de novo variants in the TOF population. These results suggest that transcriptomic datasets generated from the appropriate temporal, anatomic and cellular tissues from murine models of CHD may provide a novel approach for the prioritization of disease-contributing genes in patients with CHD.
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Affiliation(s)
- Adrianna Matos-Nieves
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, OH, United States
| | - Sathiyanarayanan Manivannan
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, OH, United States
| | - Uddalak Majumdar
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, OH, United States
| | - Kim L McBride
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, Ohio State University, Columbus, OH, United States
| | - Peter White
- Department of Pediatrics, Ohio State University, Columbus, OH, United States.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Vidu Garg
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, Ohio State University, Columbus, OH, United States.,Department of Molecular Genetics, Ohio State University, Columbus, OH, United States
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21
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Meerschaut I, Vergult S, Dheedene A, Menten B, De Groote K, De Wilde H, Muiño Mosquera L, Panzer J, Vandekerckhove K, Coucke PJ, De Wolf D, Callewaert B. A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome. Genes (Basel) 2021; 12:genes12071048. [PMID: 34356064 PMCID: PMC8304049 DOI: 10.3390/genes12071048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Copy number variations (CNVs) can modulate phenotypes by affecting protein-coding sequences directly or through interference of gene expression. Recent studies in cancer and limb defects pinpointed the relevance of non-coding gene regulatory elements such as long non-coding RNAs (lncRNAs) and topologically associated domain (TAD)-related gene-enhancer interactions. The contribution of such non-coding elements is largely unexplored in congenital heart defects (CHD). We performed a retrospective analysis of CNVs reported in a cohort of 270 CHD patients. We reviewed the diagnostic yield of pathogenic CNVs, and performed a comprehensive reassessment of 138 CNVs of unknown significance (CNV-US), evaluating protein-coding genes, lncRNA genes, and potential interferences with TAD-related gene-enhancer interactions. Fifty-two of the 138 CNV-US may relate to CHD, revealing three candidate CHD regions, 19 candidate CHD genes, 80 lncRNA genes of interest, and six potentially CHD-related TAD interferences. Our study thus indicates a potential relevance of non-coding gene regulatory elements in CNV-related CHD pathogenesis. Shortcomings in our current knowledge on genomic variation call for continuous reporting of CNV-US in international databases, careful patient counseling, and additional functional studies to confirm these preliminary findings.
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Affiliation(s)
- Ilse Meerschaut
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Katya De Groote
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Hans De Wilde
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Laura Muiño Mosquera
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Joseph Panzer
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Kristof Vandekerckhove
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Paul J. Coucke
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Daniël De Wolf
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
- Department of Pediatric Cardiology, Brussels University Hospital, 1090 Brussels, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Correspondence: ; Tel.: +32-9-332-3603
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22
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Chapman G, Moreau JLM, I P E, Szot JO, Iyer KR, Shi H, Yam MX, O'Reilly VC, Enriquez A, Greasby JA, Alankarage D, Martin EMMA, Hanna BC, Edwards M, Monger S, Blue GM, Winlaw DS, Ritchie HE, Grieve SM, Giannoulatou E, Sparrow DB, Dunwoodie SL. Functional genomics and gene-environment interaction highlight the complexity of congenital heart disease caused by Notch pathway variants. Hum Mol Genet 2021; 29:566-579. [PMID: 31813956 DOI: 10.1093/hmg/ddz270] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/05/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common birth defect and brings with it significant mortality and morbidity. The application of exome and genome sequencing has greatly improved the rate of genetic diagnosis for CHD but the cause in the majority of cases remains uncertain. It is clear that genetics, as well as environmental influences, play roles in the aetiology of CHD. Here we address both these aspects of causation with respect to the Notch signalling pathway. In our CHD cohort, variants in core Notch pathway genes account for 20% of those that cause disease, a rate that did not increase with the inclusion of genes of the broader Notch pathway and its regulators. This is reinforced by case-control burden analysis where variants in Notch pathway genes are enriched in CHD patients. This enrichment is due to variation in NOTCH1. Functional analysis of some novel missense NOTCH1 and DLL4 variants in cultured cells demonstrate reduced signalling activity, allowing variant reclassification. Although loss-of-function variants in DLL4 are known to cause Adams-Oliver syndrome, this is the first report of a hypomorphic DLL4 allele as a cause of isolated CHD. Finally, we demonstrate a gene-environment interaction in mouse embryos between Notch1 heterozygosity and low oxygen- or anti-arrhythmic drug-induced gestational hypoxia, resulting in an increased incidence of heart defects. This implies that exposure to environmental insults such as hypoxia could explain variable expressivity and penetrance of observed CHD in families carrying Notch pathway variants.
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Affiliation(s)
- Gavin Chapman
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Julie L M Moreau
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Eddie I P
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Justin O Szot
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Kavitha R Iyer
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Hongjun Shi
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,Institute for Basic Medical Sciences, Westlake University, Hangzhou, China
| | - Michelle X Yam
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | | | - Annabelle Enriquez
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, 2145, Australia.,Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Joelene A Greasby
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | | | - Ella M M A Martin
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | | | - Matthew Edwards
- Hunter Genetics, John Hunter Hospital, Newcastle, NSW, 2298, Australia.,Department of Paediatrics, School of Medicine, Western Sydney University, Sydney, NSW, 2560, Australia
| | - Steven Monger
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - Gillian M Blue
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,Kids Heart Research, Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW, 2145, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - David S Winlaw
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,Kids Heart Research, Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW, 2145, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Helen E Ritchie
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Stuart M Grieve
- Sydney Translational Imaging Laboratory, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Department of Radiology, Royal Prince Alfred Hospital, Sydney, NSW, 2050, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Duncan B Sparrow
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia.,Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
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23
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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: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Wang J, Ma X, Zhang Q, Chen Y, Wu D, Zhao P, Yu Y. The Interaction Analysis of SNP Variants and DNA Methylation Identifies Novel Methylated Pathogenesis Genes in Congenital Heart Diseases. Front Cell Dev Biol 2021; 9:665514. [PMID: 34041244 PMCID: PMC8143053 DOI: 10.3389/fcell.2021.665514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Congenital heart defect (CHD) is a rare and complicated disease with a high mortality rate. Its etiology remains unclear and includes many aspects. DNA methylation has been indicated to be involved in heart development in the early stage of life, and aberrant methylation level was related to CHDs. This study provides the first evidence of the cross talk of SNP variants and DNA methylation in clarifying CHD underlying genomic cause. We gathered whole exome sequencing (WES) data for Group 1 consisting of patients with PA (n = 78), TOF (n = 20), TAPVC (n = 78), and PDA (n = 40), and 100 healthy children as control group. Rare non-synonymous mutations and novel genes were found and highlighted. Meanwhile, we carried out the second analysis of DNA methylation data from patients with PA (n = 3), TAPVC (n = 3), TOF (n = 3), and PDA (n = 2), and five healthy controls using 850 K array in Group 2. DNA methylation was linked to WES data, and we explored an obvious overlap of hyper/hypomethylated genes. Next, we identified some candidate genes by Fisher’s exact test and Burden analysis; then, those methylated genes were figured out by the criteria of the mutation located in the CpG islands of the genome, differential methylation sites (DMS), and DNA methylation quantitative trait loci (meQTLs) in the database, respectively. Also, the interaction of differentially methylated candidate genes with known CHD pathogenetic genes was depicted in a molecular network. Taken together, our findings show that nine novel genes (ANGPTL4, VEGFA, PAX3, MUC4, HLA-DRB1, TJP2, BCR, PKD1, and HK2) in methylation level are critical to CHD and reveal a new insight into the molecular pathogenesis of CHD.
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Affiliation(s)
- Jing Wang
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China.,Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqin Ma
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China
| | - Qi Zhang
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yinghui Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Wu
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China
| | - Pengjun Zhao
- Department of Pediatric Cardiology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Yu
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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25
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Roifman M, Chung BHY, Reid DM, Teitelbaum R, Martin N, Nield LE, Thompson M, Shannon P, Chitayat D. Heterozygous NOTCH1 deletion associated with variable congenital heart defects. Clin Genet 2021; 99:836-841. [PMID: 33630301 DOI: 10.1111/cge.13948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/03/2021] [Accepted: 02/20/2021] [Indexed: 01/03/2023]
Abstract
Pathogenic heterozygous variants in the NOTCH1 gene are known to be associated with both left and right-sided congenital cardiac anomalies with strikingly incomplete penetrance and variable phenotypic expressivity. De novo NOTCH1 whole gene deletion has been reported rarely in the literature and its association with cardiac defects is less well established. Here, we report four cases of NOTCH1 gene deletion from two families associated with a spectrum of congenital heart defects from bicuspid aortic valve to complex cardiac anomalies. This is the first description of a familial NOTCH1 deletion, showing apparently high penetrance, which may be unique to this mechanism of disease. Immunohistochemical staining of cardiac tissue demonstrated reduced levels of NOTCH1 expression in both the left and right ventricular outflow tracts. These cases suggest that haploinsufficiency caused by NOTCH1 gene deletion is associated with both mild and severe cardiac defects, similar to those caused by pathogenic variants in the gene, but with apparently higher, if not complete, penetrance.
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Affiliation(s)
- Maian Roifman
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Brian Hon Yin Chung
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Department of Paediatrics and Adolescent Medicine LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Diane Myles Reid
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Ronni Teitelbaum
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Martin
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Lynne E Nield
- Division of Cardiology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Megan Thompson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Department of Fetal Pathology, Kaiser Permanente Oakland Medical Center, Oakland, California, USA
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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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 Jnl Ped Surgery 2021; 4:e000196. [DOI: 10.1136/wjps-2020-000196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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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27
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Luo S, Chen L, Wei W, Tan L, Zhang M, Duan Z, Cao J, Zhou Y, Zhou A, He X. Prenatal Genetic Diagnosis in Three Fetuses With Left Heart Hypoplasia (LHH) From Three Unrelated Families. Front Cardiovasc Med 2021; 8:631374. [PMID: 33898534 PMCID: PMC8062744 DOI: 10.3389/fcvm.2021.631374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/04/2021] [Indexed: 01/15/2023] Open
Abstract
Background: Congenital heart defects (CHDs) are the most common birth defects, and left heart hypoplasia (LHH) is a severe form of CHD and responsible for more than 20% cardiac deaths during the first week of life, however, its genetic causes remain largely elusive. Methods: Three families with fetal LHH were recruited. Genomic DNA from amniotic fluid or peripheral blood, and trio whole exome sequencing (trio-WES) and copy number variation sequencing (CNV-seq) were performed. Results: All the three couples had no family history, and mid-gestation ultrasound revealed LHH and other variable cardiovascular defects in the fetuses. Trio-WES revealed de novo pathogenic variations in KMT2D (p.Gly3465Aspfs*37) (NM_003482) and WDFY3 (p.Ser117Xfs*) (NM_014991), and CNV-seq identified a deletion of 150 kb encompassing NOTCH1. KMT2D and NOTCH1 previously have been reported to be associated with CHDs, however, WDFY3 is reported for the first time to be possibly related to CHD in human. Conclusion: Our study suggested that genetic component is an important risk factor for the development of LHH, and next generation sequencing is a powerful tool for genetic diagnosis in fetuses with CHDs and genetic counseling, however, more studies and data are need to establish the correlation of fetal phenotypes and genotypes.
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Affiliation(s)
- Sukun Luo
- Precision Medical Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Luyi Chen
- Prenatal Diagnosis Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Weizhong Wei
- Ultrasonic Diagnosis Department, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Li Tan
- Precision Medical Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Meng Zhang
- Ultrasonic Diagnosis Department, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Zhengrong Duan
- Prenatal Diagnosis Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Jiangxia Cao
- Prenatal Diagnosis Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Yan Zhou
- Prenatal Diagnosis Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Aifen Zhou
- Prenatal Diagnosis Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
| | - Xuelian He
- Precision Medical Center, Tongji Medical College, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Huazhong University of Science and Technology, Wuhan, China
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28
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Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
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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
| | | | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Sarah E. Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Hyunwoo Kim
- Department of Urology, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Patricia L. Weng
- Department of Pediatric Nephrology, University of California, Los Angeles Medical Center and University of California, Los Angeles Medical Center-Santa Monica, Los Angeles, California
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David A. Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Matthew G. Sampson
- Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts
| | - Jun Y. Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Torri
- Department of Pediatric Surgery, Spedali Civili Children’s Hospital of Brescia, Brescia, Italy
| | - Francesco Scolari
- Chair and Division of Nephrology, University and Spedali Civili Hospital, Brescia, Italy
| | - Claudia Izzi
- Division of Nephrology and Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - David E. Barton
- University College Dublin School of Medicine, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Mark G. Dobson
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Pediatric Surgery, Beacon Hospital, University College Dublin, Dublin, Ireland
| | - Susan L. Furth
- Division of Nephrology, Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Division of Nephrology, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Children’s Mercy Kansas City, Kansas City, Missouri
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Landino Allegri
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Maria Ludovica Degl'Innocenti
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Gianluigi Zaza
- Renal and Dialysis Unit, Department of Medicine, School of Medicine, University of Verona, Verona, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, Nephrology, Dialysis and Transplantation Clinics, Genoa University and IRCCS Policlinico San Martino, Genova, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, New York
| | - Ana Cristina Simões-e-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotheraphy and Management of Acute Poisoning, Pomeranian Medical University, Szczecin, Poland
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Poland
| | | | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Vladimir J. Lozanovski
- University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Zoran Gucev
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | | | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Urology, 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 Medicine, 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
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - John M. Darlow
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Cristen Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - 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
| | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
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Yusuff T, Kellaris G, Girirajan S, Katsanis N. Dissecting the complexity of CNV pathogenicity: insights from Drosophila and zebrafish models. Curr Opin Genet Dev 2021; 68:79-87. [PMID: 33812298 DOI: 10.1016/j.gde.2021.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/21/2021] [Accepted: 02/26/2021] [Indexed: 11/20/2022]
Abstract
Genetic architecture predisposes regions of the human genome to copy-number variants, which confer substantial disease risk, most prominently towards neurodevelopmental disorders. These variants typically contain multiple genes and are often associated with extensive pleiotropy and variable phenotypic expressivity. Despite the expansion of the fidelity of CNV detection, and the study of such lesions at the population level, understanding causal mechanisms for CNV phenotypes will require biological testing of constituent genes and their interactions. In this regard, model systems amenable to high-throughput phenotypic analysis of dosage-sensitive genes (and combinations thereof) are beginning to offer improved granularity of CNV-driven pathology. Here, we review the utility of Drosophila and zebrafish models for pathogenic CNV regions, highlight the advances made in discovery of single gene drivers and genetic interactions that determine specific CNV phenotypes, and argue for their validity in dissecting conserved developmental mechanisms associated with CNVs.
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30
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Kemmler CL, Riemslagh FW, Moran HR, Mosimann C. From Stripes to a Beating Heart: Early Cardiac Development in Zebrafish. J Cardiovasc Dev Dis 2021; 8:17. [PMID: 33578943 PMCID: PMC7916704 DOI: 10.3390/jcdd8020017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/18/2022] Open
Abstract
The heart is the first functional organ to form during vertebrate development. Congenital heart defects are the most common type of human birth defect, many originating as anomalies in early heart development. The zebrafish model provides an accessible vertebrate system to study early heart morphogenesis and to gain new insights into the mechanisms of congenital disease. Although composed of only two chambers compared with the four-chambered mammalian heart, the zebrafish heart integrates the core processes and cellular lineages central to cardiac development across vertebrates. The rapid, translucent development of zebrafish is amenable to in vivo imaging and genetic lineage tracing techniques, providing versatile tools to study heart field migration and myocardial progenitor addition and differentiation. Combining transgenic reporters with rapid genome engineering via CRISPR-Cas9 allows for functional testing of candidate genes associated with congenital heart defects and the discovery of molecular causes leading to observed phenotypes. Here, we summarize key insights gained through zebrafish studies into the early patterning of uncommitted lateral plate mesoderm into cardiac progenitors and their regulation. We review the central genetic mechanisms, available tools, and approaches for modeling congenital heart anomalies in the zebrafish as a representative vertebrate model.
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Affiliation(s)
| | | | | | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine and Children’s Hospital Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA; (C.L.K.); (F.W.R.); (H.R.M.)
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31
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Wyatt BH, Raymond TO, Lansdon LA, Darbro BW, Murray JC, Manak JR, Dickinson AJG. Using an aquatic model, Xenopus laevis, to uncover the role of chromodomain 1 in craniofacial disorders. Genesis 2021; 59:e23394. [PMID: 32918369 PMCID: PMC10701884 DOI: 10.1002/dvg.23394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
The chromodomain family member chromodomain 1 (CHD1) has been shown to have numerous critical molecular functions including transcriptional regulation, splicing, and DNA repair. Complete loss of function of this gene is not compatible with life. On the other hand, missense and copy number variants of CHD1 can result in intellectual disabilities and craniofacial malformations in human patients including cleft palate and Pilarowski-Bjornsson Syndrome. We have used the aquatic developmental model organism Xenopus laevis, to determine a specific role for Chd1 in such cranioafcial disorders. Protein and gene knockdown techniques in Xenopus, including antisense oligos and mosaic Crispr/Cas9-mediated mutagenesis, recapitulated the craniofacial defects observed in humans. Further analysis indicated that embryos deficient in Chd1 had defects in cranial neural crest development and jaw cartilage morphology. Additionally, flow cytometry and immunohistochemistry revealed that decreased Chd1 resulted in increased in apoptosis in the developing head. Together, these experiments demonstrate that Chd1 is critical for fundamental processes and cell survival in craniofacial development. We also presented evidence that Chd1 is regulated by retinoic acid signaling during craniofacial development. Expression levels of chd1 mRNA, specifically in the head, were increased by RAR agonist exposure and decreased upon antagonist treatment. Subphenotypic levels of an RAR antagonist and Chd1 morpholinos synergized to result in orofacial defects. Further, RAR DNA binding sequences (RAREs) were detected in chd1 regulatory regions by bioinformatic analysis. In summary, by combining human genetics and experiments in an aquatic model we now have a better understanding of the role of CHD1 in craniofacial disorders.
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Affiliation(s)
- Brent H. Wyatt
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Thomas O. Raymond
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Lisa A. Lansdon
- Department of Biology, University of Iowa, Iowa City, Iowa
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, Missouri
| | | | | | - John Robert Manak
- Department of Biology, University of Iowa, Iowa City, Iowa
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
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Song Y, Chen W, Huang Z, Tian G, Li M, Zhao Z, Feng Z, Wu F, Qian M, Ma X, Sheng W, Huang G. A Non-coding HES1 Variant Predisposes Children to Congenital Heart Disease in Chinese Population. Front Cell Dev Biol 2021; 9:631942. [PMID: 33585489 PMCID: PMC7876461 DOI: 10.3389/fcell.2021.631942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background: As a key component in the NOTCH signaling pathway, HES1 plays an important role in vertebrate heart development. Variants in the HES1 coding sequence are known to be associated with congenital heart disease (CHD). However, little is known about HES1 non-coding sequence variants and their association with the risk of developing CHD. Method and Results: We initially analyzed the non-coding sequence of the HES1 gene in 12 unrelated CHD families by direct sequencing and identified a previously unreported promoter region variant (NM_005524.4: c.-1279-1278 insAC, rs148941464) in the HES1 gene in four CHD families. The homozygous variant in patients was inherited from carrier parents with normal phenotypes, indicating a likely recessive genetic model. Given that the HES1 gene is predicted to be likely to exhibit haploinsufficiency (%HI: 11.44), we hypothesized that the HES1 homozygous variant is a genetic risk factor underlying CHD. We then carried out sequencing of this HES1 variant in 629 sporadic non-syndromic CHD cases and 696 healthy controls and performed association analysis. Interestingly, we observed a significant association of the homozygous HES1 promoter variant with CHD (18.92% of cases vs. 9.91% of controls; OR: 2.291, 95% CI: 1.637-3.207, p = 9.72 × 10-7). No significant association with CHD was observed for the HES1 promoter heterozygous variant (p > 0.05). However, association analysis tests of the HES1 homozygous variant with each subtype of CHD revealed that this homozygous variant was strongly associated with transposition of the great arteries (TGA) (OR: 3.726, 95% CI: 1.745-7.956, p = 0.0003). Moreover, the prevalence of HES1 homozygous variants in CHD patients with TGA (27.66%) was significantly higher than that in patients with other CHD subtypes or controls. Similar results were observed in a replication group of TGA (n = 64). Functional studies demonstrated that the homozygous variant in the HES1 promoter can disrupt its ability to bind RXRA, an inhibitory transcription factor, which results in abnormally high expression of the HES1 gene, indicating that this variant harbors gain-of-function effects. Conclusions: Our findings reveal that the non-coding homozygous variant in the HES1 promoter has a gain-of-function effect and is associated with an increased risk of CHD development, especially the severe TGA subtype.
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Affiliation(s)
- Yangliu Song
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China
| | - Weicheng Chen
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China
| | - Zitong Huang
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Guixiang Tian
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Mengru Li
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Zhengshan Zhao
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Zhiyu Feng
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China
| | - Feizhen Wu
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China
| | - Maoxiang Qian
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China
| | - Xiaojing Ma
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China
| | - Wei Sheng
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Guoying Huang
- Institutes of Biomedical Sciences, and Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
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Kim RW. Is There Any Clinical Utility to Genetic Testing for Patients With Congenital Heart Disease? Semin Thorac Cardiovasc Surg Pediatr Card Surg Annu 2021; 24:26-29. [PMID: 34116779 DOI: 10.1053/j.pcsu.2021.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/11/2021] [Accepted: 04/19/2021] [Indexed: 11/11/2022]
Abstract
Genetic diagnosis is becoming increasingly sophisticated, with the ability to identify even fine differences in patients with a wide variety of congenital heart lesions. Although we have an incomplete understanding of the clinical consequences of most genetic findings, some categories of mutations can have important implications for disease recurrence and prognosis. Consideration of the biology underlying a genetic deficiency, when known, can be useful in the clinical management of some patients.
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Affiliation(s)
- Richard W Kim
- Pediatric and Congenital Cardiac Surgery, Guerin Congenital Heart Program, Smidt Heart Institute, Cedars- Sinai Medical Center, Los Angeles, California.
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34
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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35
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Shi SS, Lin SB, Cai DL, Wen WR, Li RM. Discordance of cardiovascular abnormalities in a monozygotic twin pair carrying a class II 1q21.1 microdeletion. Taiwan J Obstet Gynecol 2020; 59:123-126. [PMID: 32039779 DOI: 10.1016/j.tjog.2019.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE We present the prenatal diagnosis of a class II 1q21.1 microdeletion in monozygotic (MZ) twins with discordant phenotypes. CASE REPORT A monochorionic diamniotic twin pair presented with discordant ultrasound anomalies; twin A had cardiovascular abnormalities, while twin B did not. No specific complications were noted in the twins during pregnancy. A single nucleotide polymorphism array revealed an identical class II 1q21.1 microdeletion inherited from a phenotypically normal mother and identified the twins as MZ. The deleted region encompassed both the proximal 1q21.1 thrombocytopenia absent radius syndrome region and the distal 1q21.1 recurrent microdeletion region. No other rare copy number variants (CNVs) were identified, and concordance was observed in the CNVs between the twins. CONCLUSION Discordant cardiovascular abnormalities may occur in MZ twins carrying the same class II 1q21.1 microdeletion. Further studies involving discordant MZ twins are needed to determine the modifying factors of the phenotypic heterogeneity of the microdeletion.
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Affiliation(s)
- Shan-Shan Shi
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China
| | - Shao-Bin Lin
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Dan-Lei Cai
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wang-Rong Wen
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China.
| | - Rui-Man Li
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China.
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Abstract
Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer. Accurate variant calling in NGS data is a critical step upon which virtually all downstream analysis and interpretation processes rely. Just as NGS technologies have evolved considerably over the past 10 years, so too have the software tools and approaches for detecting sequence variants in clinical samples. In this review, I discuss the current best practices for variant calling in clinical sequencing studies, with a particular emphasis on trio sequencing for inherited disorders and somatic mutation detection in cancer patients. I describe the relative strengths and weaknesses of panel, exome, and whole-genome sequencing for variant detection. Recommended tools and strategies for calling variants of different classes are also provided, along with guidance on variant review, validation, and benchmarking to ensure optimal performance. Although NGS technologies are continually evolving, and new capabilities (such as long-read single-molecule sequencing) are emerging, the “best practice” principles in this review should be relevant to clinical variant calling in the long term.
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Affiliation(s)
- Daniel C Koboldt
- Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, USA. .,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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37
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Yang T, Huang Z, Li H, Wang L, Chen Y. Conjugated activation of myocardial-specific transcription of Gja5 by a pair of Nkx2-5-Shox2 co-responsive elements. Dev Biol 2020; 465:79-87. [PMID: 32687896 DOI: 10.1016/j.ydbio.2020.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023]
Abstract
The sinoatrial node (SAN) is the primary pacemaker in the heart. During cardiogenesis, Shox2 and Nkx2-5 are co-expressed in the junction domain of the SAN and regulate pacemaker cell fate through a Shox2-Nkx2-5 antagonism. Cx40 is a marker of working myocardium and an Nkx2-5 transcriptional output antagonized by Shox2, but the underlying regulatory mechanisms remain elusive. Here we characterized a bona fide myocardial-specific Gja5 (coding gene of Cx40) distal enhancer consisting of a pair of Nkx2-5 and Shox2 co-bound elements in the regulatory region of Gja5. Transgenic reporter assays revealed that neither element alone, but the conjugation of both elements together, drives myocardial-specific transcription. Genetic analyses confirmed that the activation of this enhancer depends on Nkx2-5 but is inhibited by Shox2 in vivo, and its presence is essential for Gja5 expression in the myocardium but not the endothelial cells of the heart. Furthermore, chromatin conformation analysis showed an Nkx2-5-dependent loop formation between these two elements and the Gja5 promoter in vivo, indicating that Nkx2-5 bridges the conjugated activation of this enhancer by pairing the two elements to the Gja5 promoter.
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38
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Kozyrev I, Dokshin P, Kostina A, Kiselev A, Ignatieva E, Golovkin A, Pervunina T, Grekhov E, Gordeev M, Kostareva A, Malashicheva A. Dysregulation of Notch signaling in cardiac mesenchymal cells of patients with tetralogy of Fallot. Pediatr Res 2020; 88:38-47. [PMID: 31952074 DOI: 10.1038/s41390-020-0760-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 01/17/2023]
Abstract
BACKGROUND Tetralogy of Fallot (TF) is a severe congenital defect of heart development. Fine-tuned sequential activation of Notch signaling genes is responsible for proper heart chamber development. Mutations in Notch genes have been associated with TF. The aim of this study was to analyze the activity of the Notch pathway in cardiac mesenchymal cells derived from ventricular tissue of TF patients. METHODS Cardiac mesenchymal cells were isolated from 42 TF patients and from 14 patients with ventricular septal defects (VSDs), used as a comparison group. The Notch pathway was analyzed by estimating the expression of Notch-related genes by qPCR. Differentiation and proliferation capacity of the cells was estimated. RESULTS The TF-derived cells demonstrated a dysregulated pattern of Notch-related gene expression comparing to VSD-derived cells. Correlation of Notch signaling activation level by HEY1/HES1 expression level with proliferation and cardiogenic-like differentiation of cardiac mesenchymal cells was observed but not with clinical parameters nor with the age of the patients. CONCLUSIONS The data suggest a contribution of dysregulated Notch signaling to the pathogenesis of tetralogy of Fallot and importance of Notch signaling level for the functional state of cardiac mesenchymal cells, which could be critical considering these cells for potential cell therapy approaches.
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39
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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. Circ Genom Precis Med 2020; 13:e002836. [PMID: 32812804 PMCID: PMC7439931 DOI: 10.1161/circgen.119.002836] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect, found in up to 2% of the population and associated with a 30% lifetime risk of complications. BAV is inherited as an autosomal dominant trait with incomplete penetrance and variable expressivity due to a complex genetic architecture that involves many interacting genes. In this review, we highlight the current state of knowledge about BAV genetics, principles and methods for BAV gene discovery, clinical applications of BAV genetics, and important future directions.
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41
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Yusuff T, Jensen M, Yennawar S, Pizzo L, Karthikeyan S, Gould DJ, Sarker A, Gedvilaite E, Matsui Y, Iyer J, Lai ZC, Girirajan S. Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PLoS Genet 2020; 16:e1008792. [PMID: 32579612 PMCID: PMC7313740 DOI: 10.1371/journal.pgen.1008792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/23/2020] [Indexed: 11/25/2022] Open
Abstract
While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non-neuronal phenotypes, functional studies evaluating these regions have focused on the molecular basis of neuronal defects. We report a systematic functional analysis of non-neuronal defects for homologs of 59 genes within ten pathogenic CNVs and 20 neurodevelopmental genes in Drosophila melanogaster. Using wing-specific knockdown of 136 RNA interference lines, we identified qualitative and quantitative phenotypes in 72/79 homologs, including 21 lines with severe wing defects and six lines with lethality. In fact, we found that 10/31 homologs of CNV genes also showed complete or partial lethality at larval or pupal stages with ubiquitous knockdown. Comparisons between eye and wing-specific knockdown of 37/45 homologs showed both neuronal and non-neuronal defects, but with no correlation in the severity of defects. We further observed disruptions in cell proliferation and apoptosis in larval wing discs for 23/27 homologs, and altered Wnt, Hedgehog and Notch signaling for 9/14 homologs, including AATF/Aatf, PPP4C/Pp4-19C, and KIF11/Klp61F. These findings were further supported by tissue-specific differences in expression patterns of human CNV genes, as well as connectivity of CNV genes to signaling pathway genes in brain, heart and kidney-specific networks. Our findings suggest that multiple genes within each CNV differentially affect both global and tissue-specific developmental processes within conserved pathways, and that their roles are not restricted to neuronal functions. Rare copy-number variants (CNVs), or large deletions and duplications in the genome, are associated with both neuronal and non-neuronal clinical features. Previous functional studies for these disorders have primarily focused on understanding the cellular mechanisms for neurological and behavioral phenotypes. To understand how genes within these CNVs contribute to developmental defects in non-neuronal tissues, we assessed 79 homologs of CNV and known neurodevelopmental genes in Drosophila models. We found that most homologs showed developmental defects when knocked down in the adult fly wing, ranging from mild size changes to severe wrinkled wings or lethality. Although a majority of tested homologs showed defects when knocked down specifically in wings or eyes, we found no correlation in the severity of the observed defects in these two tissues. A subset of the homologs showed disruptions in cellular processes in the developing fly wing, including alterations in cell proliferation, apoptosis, and cellular signaling pathways. Furthermore, human CNV genes also showed differences in gene expression patterns and interactions with signaling pathway genes across multiple human tissues. Our findings suggest that genes within CNV disorders affect global developmental processes in both neuronal and non-neuronal tissues.
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Affiliation(s)
- Tanzeen Yusuff
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Siddharth Karthikeyan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dagny J. Gould
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Avik Sarker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Erika Gedvilaite
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yurika Matsui
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Janani Iyer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Zhi-Chun Lai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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Bekpen C, Tautz D. Human core duplicon gene families: game changers or game players? Brief Funct Genomics 2020; 18:402-411. [PMID: 31529038 PMCID: PMC6920530 DOI: 10.1093/bfgp/elz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/01/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023] Open
Abstract
Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available for 10 such families and include some new analyses. A picture emerges that suggests broad functions for these protein families, possibly through modification of core cellular pathways. Still, more dedicated studies are required to elucidate the function of core-duplicons gene families and how they have shaped adaptations and evolution of humans.
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Affiliation(s)
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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Wang Y, Jiang T, Tang P, Wu Y, Jiang Z, Dai J, Gu Y, Xu J, Da M, Ma H, Jin G, Mo X, Li Q, Wang X, Hu Z. Family-based whole-genome sequencing identifies compound heterozygous protein-coding and noncoding mutations in tetralogy of Fallot. Gene 2020; 741:144555. [PMID: 32165302 DOI: 10.1016/j.gene.2020.144555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/08/2020] [Indexed: 12/28/2022]
Abstract
Tetralogy of Fallot (TOF) is one of most serious cyanotic congenital heart disease (CHD) and the prevalence is estimated to be 1 in 3000 live births worldwide. Though multiple studies have found genetic variants as risk factors for TOF, they could only explain a small fraction of the pathogenesis. Here, we performed whole genome sequencing (WGS) for 6 individuals derived from 2 families to evaluate pathogenic mutations located in both coding and noncoding regions. We characterized the annotated deleterious coding mutations and impaired noncoding mutations in regulatory elements by various data analysis. Additionally, functional assays were conducted to validate function regulatory elements and noncoding mutations. Interestingly, a compound heterozygous pattern with pathogenic coding and noncoding mutations was identified in probands. In proband 1, biallelic mutations (g.139409115A > T, encoding p.Asn685Ile; g.139444949C > A) in NOTCH1 exon and its regulatory element were detected. In vitro experiments revealed that the regulatory element acted as a silencer and the noncoding mutation decreased the expression of NOTCH1. In proband 2, we also found compound heterozygous mutations (g. 216235029C > T, encoding p.Val2281Met; g. 216525154A > C) which potentially regulated the function of FN1 gene. In summary, our study firstly reported an instance of newly identified noncoding mutation in regulatory element within the compound heterozygous pattern in TOF. The results provided a deeper understanding of TOF genetic architectures.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Pushi Tang
- Department of Cardiovascular Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Yifei Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhu Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Jing Xu
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Min Da
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xuming Mo
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Qingguo Li
- Department of Cardiovascular Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China.
| | - Xiaowei Wang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China.
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44
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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45
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Lalani SR. Other genomic disorders and congenital heart disease. Am J Med Genet 2020; 184:107-115. [DOI: 10.1002/ajmg.c.31762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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46
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Nees SN, Chung WK. The genetics of isolated congenital heart disease. Am J Med Genet C Semin Med Genet 2019; 184:97-106. [PMID: 31876989 DOI: 10.1002/ajmg.c.31763] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/06/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022]
Abstract
The genetic mechanisms underlying congenital heart disease (CHD) are complex and remain incompletely understood. The majority of patients with CHD have an isolated heart defect without other organ system involvement, but the genetic basis of isolated CHD has been even more difficult to elucidate compared to syndromic CHD. Our understanding of the genetics of isolated CHD is advancing in large part due to advances in next generation sequencing, and the list of genes associated with CHD is rapidly expanding. Variants in hundreds of genes have been identified that may cause or contribute to CHD, but a genetic cause can still only be identified in about 20-30% of patients. Identifying a genetic cause for CHD can have an impact on clinical outcomes and prognosis and thus it is important for clinicians to understand when and what to test in patients with isolated CHD. This chapter reviews some of the known genetic mechanisms that contribute to isolated inherited and sporadic CHD as well as recommendations for evaluation and genetic testing in patients with isolated CHD.
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Affiliation(s)
- Shannon N Nees
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York.,Department of Medicine, Columbia University Irving Medical Center, New York, New York
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Dasouki MJ, Wakil SM, Al-Harazi O, Alkorashy M, Muiya NP, Andres E, Hagos S, Aldusery H, Dzimiri N, Colak D. New Insights into the Impact of Genome-Wide Copy Number Variations on Complex Congenital Heart Disease in Saudi Arabia. OMICS 2019; 24:16-28. [PMID: 31855513 DOI: 10.1089/omi.2019.0165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Congenital heart diseases (CHDs) are complex traits that manifest in diverse clinical phenotypes such as the Tetralogy of Fallot (TOF), valvular and ventricular/atrial septal defects. Genetic mechanisms of CHDs have remained largely unclear to date. Copy number variations (CNVs) have been implicated in many complex diseases but their impact has not been examined extensively in various forms of CHD lesions. We report in this study, to the best of our knowledge, the largest cohort of Saudi Arab CHD patients to date who were evaluated using genome-wide CNV analysis. In a sample of 134 Saudi Arab patients with CHD, 66 exhibited pathogenic or likely pathogenic CNVs. Notably, 21 copy number gains and 11 copy number losses were detected that encompassed 141 genes and 146 genes, respectively. The most frequent gains were on 17q21.31, 8p11.21, and 22q11.23, whereas the losses were primarily localized to 16p11.2. Interestingly, all lesions have had gains at 17q21.31. Septal defects had also gains at 8p11.21 and 22q11.23, valvular lesions at 8p11.21, 22q11.23, and 2q13, and TOF at 16p11.2. Functional and network analyses demonstrated that cardiovascular and nervous system development and function as well as cell death/survival were most significantly associated with CNVs, thus highlighting the potentially important genes likely to be involved in CHD, including NPHP1, PLCB1, KANSL1, and NR3C1. In conclusion, this genome-wide analysis identifies a high frequency of CNVs mostly in patients with septal defects, primarily influencing cardiovascular developmental and functional pathways, thereby offering a deeper insight into the complex networks involved in CHD pathogenesis.
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Affiliation(s)
- Majed J Dasouki
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Olfat Al-Harazi
- Departments Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maarab Alkorashy
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nzioka P Muiya
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Editha Andres
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya Hagos
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Haya Aldusery
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nduna Dzimiri
- Departments Genetics and Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dilek Colak
- Departments Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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Page DJ, Miossec MJ, Williams SG, Monaghan RM, Fotiou E, Cordell HJ, Sutcliffe L, Topf A, Bourgey M, Bourque G, Eveleigh R, Dunwoodie SL, Winlaw DS, Bhattacharya S, Breckpot J, Devriendt K, Gewillig M, Brook JD, Setchfield KJ, Bu'Lock FA, O'Sullivan J, Stuart G, Bezzina CR, Mulder BJM, Postma AV, Bentham JR, Baron M, Bhaskar SS, Black GC, Newman WG, Hentges KE, Lathrop GM, Santibanez-Koref M, Keavney BD. Whole Exome Sequencing Reveals the Major Genetic Contributors to Nonsyndromic Tetralogy of Fallot. Circ Res 2019; 124:553-563. [PMID: 30582441 DOI: 10.1161/circresaha.118.313250] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Familial recurrence studies provide strong evidence for a genetic component to the predisposition to sporadic, nonsyndromic Tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease phenotype. Rare genetic variants have been identified as important contributors to the risk of congenital heart disease, but relatively small numbers of TOF cases have been studied to date. OBJECTIVE We used whole exome sequencing to assess the prevalence of unique, deleterious variants in the largest cohort of nonsyndromic TOF patients reported to date. METHODS AND RESULTS Eight hundred twenty-nine TOF patients underwent whole exome sequencing. The presence of unique, deleterious variants was determined; defined by their absence in the Genome Aggregation Database and a scaled combined annotation-dependent depletion score of ≥20. The clustering of variants in 2 genes, NOTCH1 and FLT4, surpassed thresholds for genome-wide significance (assigned as P<5×10-8) after correction for multiple comparisons. NOTCH1 was most frequently found to harbor unique, deleterious variants. Thirty-one changes were observed in 37 probands (4.5%; 95% CI, 3.2%-6.1%) and included 7 loss-of-function variants 22 missense variants and 2 in-frame indels. Sanger sequencing of the unaffected parents of 7 cases identified 5 de novo variants. Three NOTCH1 variants (p.G200R, p.C607Y, and p.N1875S) were subjected to functional evaluation, and 2 showed a reduction in Jagged1-induced NOTCH signaling. FLT4 variants were found in 2.4% (95% CI, 1.6%-3.8%) of TOF patients, with 21 patients harboring 22 unique, deleterious variants. The variants identified were distinct to those that cause the congenital lymphoedema syndrome Milroy disease. In addition to NOTCH1, FLT4 and the well-established TOF gene, TBX1, we identified potential association with variants in several other candidates, including RYR1, ZFPM1, CAMTA2, DLX6, and PCM1. CONCLUSIONS The NOTCH1 locus is the most frequent site of genetic variants predisposing to nonsyndromic TOF, followed by FLT4. Together, variants in these genes are found in almost 7% of TOF patients.
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Affiliation(s)
- Donna J Page
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Matthieu J Miossec
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.).,Center for Bioinformatics and Integrative Biology, Faculty of Biological Sciences, Universidad Andrés Bello, Santiago, Chile (M.J.M.)
| | - Simon G Williams
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Richard M Monaghan
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Elisavet Fotiou
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | | | - Ana Topf
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, Montréal, QC, Canada (M.B.).,McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Guillaume Bourque
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Robert Eveleigh
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Sally L Dunwoodie
- Chain Reaction Program in Congenital Heart Disease Research, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia (S.L.D.).,Faculties of Medicine and Science, University of New South Wales, Sydney (S.L.D.).,Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW (S.L.D.)
| | - David S Winlaw
- School of Child and Adolescent Health, Sydney Medical School, University of Sydney (D.S.W.).,Victor Chang Cardiac Research Institute, NSW, Australia (D.S.W.).,RDM Cardiovascular Medicine, Wellcome Centre for Human Genetics, University of Oxford (D.S.W., S.B.)
| | - Shoumo Bhattacharya
- RDM Cardiovascular Medicine, Wellcome Centre for Human Genetics, University of Oxford (D.S.W., S.B.).,Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.)
| | - Jeroen Breckpot
- Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.).,Pediatric and Congenital Cardiology, UZ Leuven (J.B., M.G.)
| | - Koenraad Devriendt
- Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.)
| | - Marc Gewillig
- Pediatric and Congenital Cardiology, UZ Leuven (J.B., M.G.)
| | - J David Brook
- School of Life Sciences, University of Nottingham, Queen's Medical Centre (J.D.B., K.J.S.)
| | - Kerry J Setchfield
- School of Life Sciences, University of Nottingham, Queen's Medical Centre (J.D.B., K.J.S.)
| | - Frances A Bu'Lock
- Congenital and Paediatric Cardiology, East Midlands Congenital Heart Centre and University of Leicester, Glenfield Hospital (F.A.B.)
| | - John O'Sullivan
- Adult Congenital and Paediatric Cardiac Unit, Freeman Hospital, Newcastle upon Tyne (J.O.)
| | - Graham Stuart
- University Hospitals Bristol NHS Foundation Trust, Bristol (G.S.)
| | - Connie R Bezzina
- Heart Center, Department of Clinical and Experimental Cardiology (C.R.B.), Academic Medical Center, Amsterdam, the Netherlands
| | - Barbara J M Mulder
- Department of Medical Biology (B.J.M.M.), Academic Medical Center, Amsterdam, the Netherlands
| | - Alex V Postma
- Department of Clinical Genetics (A.V.P.), Academic Medical Center, Amsterdam, the Netherlands
| | - James R Bentham
- Department of Paediatric Cardiology, Yorkshire Heart Centre, Leeds (J.R.B.)
| | - Martin Baron
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester (M.B.)
| | - Sanjeev S Bhaskar
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford, Manchester (S.S.B., G.C.B.)
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford, Manchester (S.S.B., G.C.B.)
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford (W.G.N.); and Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, UK
| | | | - G Mark Lathrop
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Mauro Santibanez-Koref
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | - Bernard D Keavney
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
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Fotiou E, Williams S, Martin-Geary A, Robertson DL, Tenin G, Hentges KE, Keavney B. Integration of Large-Scale Genomic Data Sources With Evolutionary History Reveals Novel Genetic Loci for Congenital Heart Disease. Circ Genom Precis Med 2019; 12:442-451. [PMID: 31613678 PMCID: PMC6798745 DOI: 10.1161/circgen.119.002694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Supplemental Digital Content is available in the text. Most cases of congenital heart disease (CHD) are sporadic and nonsyndromic, with poorly understood etiology. Rare genetic variants have been found to affect the risk of sporadic, nonsyndromic CHD, but individual studies to date are of only moderate sizes, and none to date has incorporated the ohnolog status of candidate genes in the analysis. Ohnologs are genes retained from ancestral whole-genome duplications during evolution; multiple lines of evidence suggest ohnologs are overrepresented among dosage-sensitive genes. We integrated large-scale data on rare variants with evolutionary information on ohnolog status to identify novel genetic loci predisposing to CHD.
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Affiliation(s)
- Elisavet Fotiou
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester
| | - Simon Williams
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester
| | - Alexandra Martin-Geary
- Division of Evolution and Genomic science (A.M.-G., D.L.R., K.E.H.), University of Manchester
| | - David L Robertson
- Division of Evolution and Genomic science (A.M.-G., D.L.R., K.E.H.), University of Manchester.,MRC-University of Glasgow Centre for Virus Research (D.L.R.)
| | - Gennadiy Tenin
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester
| | - Kathryn E Hentges
- Division of Evolution and Genomic science (A.M.-G., D.L.R., K.E.H.), University of Manchester
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre (E.F., S.W., G.T., B.K.), University of Manchester.,Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester (B.K.)
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50
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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