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Feldman ER, Li Y, Cutler DJ, Rosser TC, Wechsler SB, Sanclemente L, Rachubinski AL, Elliott N, Vyas P, Roberts I, Rabin KR, Wagner M, Gelb BD, Espinosa JM, Lupo PJ, de Smith AJ, Sherman SL, Leslie EJ. Genome-wide association studies of Down syndrome associated congenital heart defects. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.06.24313183. [PMID: 39281767 PMCID: PMC11398599 DOI: 10.1101/2024.09.06.24313183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Congenital heart defects (CHDs) are the most common structural birth defect and are present in 40-50% of children born with Down syndrome (DS). To characterize the genetic architecture of DS-associated CHD, we sequenced genomes of a multiethnic group of children with DS and a CHD (n=886: atrioventricular septal defects (AVSD), n=438; atrial septal defects (ASD), n=122; ventricular septal defects (VSD), n=170; other types of CHD, n=156) and DS with a structurally normal heart (DS+NH, n=572). We performed four GWAS for common variants (MAF>0.05) comparing DS with CHD, stratified by CHD-subtype, to DS+NH controls. Although no SNP achieved genome-wide significance, multiple loci in each analysis achieved suggestive significance (p<2×10-6). Of these, the 1p35.1 locus (near RBBP4) was specifically associated with ASD risk and the 5q35.2 locus (near MSX2) was associated with any type of CHD. Each of the suggestive loci contained one or more plausible candidate genes expressed in the developing heart. While no SNP replicated (p<2×10-6) in an independent cohort of DS+CHD (DS+CHD: n=229; DS+NH: n=197), most SNPs that were suggestive in our GWASs remained suggestive when meta-analyzed with the GWASs from the replication cohort. These results build on previous work to identify genetic modifiers of DS-associated CHD.
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Affiliation(s)
- Elizabeth R Feldman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322
| | - Yunqi Li
- Center for Genetic Epidemiology, Keck School of Medicine of University of Southern California, Los Angeles, CA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322
| | - Tracie C Rosser
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322
| | - Stephanie B Wechsler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322
| | | | - Angela L Rachubinski
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Natalina Elliott
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Paresh Vyas
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Irene Roberts
- Department of Paediatrics and MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | | | - Michael Wagner
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Bruce D Gelb
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Adam J de Smith
- Center for Genetic Epidemiology, Keck School of Medicine of University of Southern California, Los Angeles, CA
| | - Stephanie L Sherman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322
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Nawaz K, Alifah N, Hussain T, Hameed H, Ali H, Hamayun S, Mir A, Wahab A, Naeem M, Zakria M, Pakki E, Hasan N. From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies. Curr Probl Cardiol 2024; 49:102726. [PMID: 38944223 DOI: 10.1016/j.cpcardiol.2024.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.
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Affiliation(s)
- Khalid Nawaz
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Nur Alifah
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Talib Hussain
- Women Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Hameed
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Haider Ali
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Awal Mir
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Mohammad Zakria
- Advanced Center for Genomic Technologies, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Ermina Pakki
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia.
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Broberg M, Ampuja M, Jones S, Ojala T, Rahkonen O, Kivelä R, Priest J, Palotie A, Ollila HM, Helle E. Genome-wide association studies highlight novel risk loci for septal defects and left-sided congenital heart defects. BMC Genomics 2024; 25:256. [PMID: 38454350 PMCID: PMC10918883 DOI: 10.1186/s12864-024-10172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/28/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Congenital heart defects (CHD) are structural defects of the heart affecting approximately 1% of newborns. They exhibit low penetrance and non-Mendelian patterns of inheritance as varied and complex traits. While genetic factors are known to play an important role in the development of CHD, the specific genetics remain unknown for the majority of patients. To elucidate the underlying genetic risk, we performed a genome wide association study (GWAS) of CHDs in general and specific CHD subgroups using the FinnGen Release 10 (R10) (N > 393,000), followed by functional fine-mapping through eQTL and co-localization analyses using the GTEx database. RESULTS We discovered three genome-wide significant loci associated with general CHD. Two of them were located in chromosome 17: 17q21.32 (rs2316327, intronic: LRRC37A2, Odds ratio (OR) [95% Confidence Interval (CI)] = 1.17[1.12-1.23], p = 1.5 × 10-9) and 17q25.3 (rs1293973611, nearest: BAHCC1, OR[95%CI] = 4.48[2.80-7.17], p = 7.0 × 10-10), respectively, and in addition to general CHD, the rs1293973611 locus was associated with the septal defect subtype. The third locus was in band 1p21.2 (rs35046143, nearest: PALMD, OR[95%CI] = 1.15[1.09-1.21], p = 7.1 × 10-9), and it was associated with general CHD and left-sided lesions. In the subgroup analysis, two additional loci were associated with septal defects (rs75230966 and rs6824295), and one with left-sided lesions (rs1305393195). In the eQTL analysis the variants rs2316327 (general CHD), and rs75230966 (septal defects) both located in 17q21.32 (with a LD r2 of 0.41) were both predicted to significantly associate with the expression of WNT9B in the atrial appendage tissue category. This effect was further confirmed by co-localization analysis, which also implicated WNT3 expression in the atrial appendage. A meta-analysis of general CHD together with the UK Biobank (combined N = 881,678) provided a different genome-wide significant locus in LRRC37A2; rs16941382 (OR[95%CI] = 1.15[1.11-1.20], p = 1.5 × 10-9) which is in significant LD with rs2316327. CONCLUSIONS Our results of general CHD and different CHD subcategories identified a complex risk locus on chromosome 17 near BAHCC1 and LRRC37A2, interacting with the genes WNT9B, WNT3 and MYL4, may constitute potential novel CHD risk associated loci, warranting future experimental tests to determine their role.
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Affiliation(s)
- Martin Broberg
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Minna Ampuja
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Samuel Jones
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Tiina Ojala
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Otto Rahkonen
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Riikka Kivelä
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Wihuri Research Institute, 00290, Helsinki, Finland
- Faculty of Sport and Health Sciences, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - James Priest
- School of Medicine, Stanford University, Stanford University, Stanford, CA, 94305, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Emmi Helle
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland.
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland.
- , Haartmaninkatu 8, Helsinki, 00014, Finland.
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, 00271, Finland.
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Dorn C, Perrot A, Grunert M, Rickert-Sperling S. Human Genetics of Tetralogy of Fallot and Double-Outlet Right Ventricle. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:629-644. [PMID: 38884738 DOI: 10.1007/978-3-031-44087-8_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Tetralogy of Fallot (TOF) and double-outlet right ventricle (DORV) are conotruncal defects resulting from disturbances of the second heart field and the neural crest, which can occur as isolated malformations or as part of multiorgan syndromes. Their etiology is multifactorial and characterized by overlapping genetic causes. In this chapter, we present the different genetic alterations underlying the two diseases, which range from chromosomal abnormalities like aneuploidies and structural mutations to rare single nucleotide variations affecting distinct genes. For example, mutations in the cardiac transcription factors NKX2-5, GATA4, and HAND2 have been identified in isolated TOF cases, while mutations of TBX5 and 22q11 deletion, leading to haploinsufficiency of TBX1, cause Holt-Oram and DiGeorge syndrome, respectively. Moreover, genes involved in signaling pathways, laterality determination, and epigenetic mechanisms have also been found mutated in TOF and/or DORV patients. Finally, genome-wide association studies identified common single nucleotide polymorphisms associated with the risk for TOF.
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Affiliation(s)
- Cornelia Dorn
- Cardiovascular Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Perrot
- Cardiovascular Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel Grunert
- Cardiovascular Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
- DiNAQOR AG, Schlieren, Switzerland
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Kukshal P, Joshi RO, Kumar A, Ahamad S, Murthy PR, Sathe Y, Manohar K, Guhathakurta S, Chellappan S. Case-control association study of congenital heart disease from a tertiary paediatric cardiac centre from North India. BMC Pediatr 2023; 23:290. [PMID: 37322441 PMCID: PMC10268439 DOI: 10.1186/s12887-023-04095-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/27/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Congenital Heart diseases (CHDs) account for 1/3rd of all congenital birth defects. Etiopathogenesis of CHDs remain elusive despite extensive investigations globally. Phenotypic heterogeneity witnessed in this developmental disorder reiterate gene-environment interactions with periconceptional factors as risk conferring; and genetic analysis of both sporadic and familial forms of CHD suggest its multigenic basis. Significant association of de novo and inherited variants have been observed. Approximately 1/5th of CHDs are documented in the ethnically distinct Indian population but genetic insights have been very limited. This pilot case-control based association study was undertaken to investigate the status of Caucasian SNPs in a north Indian cohort. METHOD A total of 306 CHD cases sub-classified into n = 198 acyanotic and n = 108 cyanotic types were recruited from a dedicated tertiary paediatric cardiac centre in Palwal, Haryana. 23 SNPs primarily prioritized from Genome-wide association studies (GWAS) on Caucasians were genotyped using Agena MassARRAY Technology and test of association was performed with adequately numbered controls. RESULTS Fifty percent of the studied SNPs were substantially associated in either allelic, genotypic or sub-phenotype categories validating their strong correlation with disease manifestation. Of note, strongest allelic association was observed for rs73118372 in CRELD1 (p < 0.0001) on Chr3, rs28711516 in MYH6 (p = 0.00083) and rs735712 in MYH7 (p = 0.0009) both on Chr 14 and were also significantly associated with acyanotic, and cyanotic categories separately. rs28711516 (p = 0.003) and rs735712 (p = 0.002) also showed genotypic association. Strongest association was observed with rs735712(p = 0.003) in VSD and maximum association was observed for ASD sub-phenotypes. CONCLUSIONS Caucasian findings were partly replicated in the north Indian population. The findings suggest the contribution of genetic, environmental and sociodemographic factors, warranting continued investigations in this study population.
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Affiliation(s)
- Prachi Kukshal
- Sri Sathya Sai Sanjeevani Research Foundation, NH-2, Delhi-Mathura Highway, Baghola, Haryana, District Palwal, Pin- 121102, India.
| | - Radha O Joshi
- Present address Sri Sathya Sai Sanjeevani Research Foundation, Kharghar, Navi Mumbai- 410210, Maharashtra, India
| | - Ajay Kumar
- Sri Sathya Sai Sanjeevani Research Foundation, NH-2, Delhi-Mathura Highway, Baghola, Haryana, District Palwal, Pin- 121102, India
| | - Shadab Ahamad
- Sri Sathya Sai Sanjeevani Research Foundation, NH-2, Delhi-Mathura Highway, Baghola, Haryana, District Palwal, Pin- 121102, India
| | - Prabhatha Rashmi Murthy
- Sri Sathya Sai Sanjeevani Centre for Child Heart Care and Training in Paediatric Cardiac Skills, Navi Mumbai Maharashtra, India
| | - Yogesh Sathe
- Sri Sathya Sai Sanjeevani International Centre for Child Heart Care & Research, NH-2, Delhi-Mathura Highway, Baghola, District Palwal, Haryana, Pin 121102, India
| | - Krishna Manohar
- Sri Sathya Sai Sanjeevani International Centre for Child Heart Care & Research, NH-2, Delhi-Mathura Highway, Baghola, District Palwal, Haryana, Pin 121102, India
| | - Soma Guhathakurta
- Sri Sathya Sai Sanjeevani Research Foundation, NH-2, Delhi-Mathura Highway, Baghola, Haryana, District Palwal, Pin- 121102, India
| | - Subramanian Chellappan
- Sri Sathya Sai Sanjeevani International Centre for Child Heart Care & Research, NH-2, Delhi-Mathura Highway, Baghola, District Palwal, Haryana, Pin 121102, India.
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Zhu W, Lo CW. Insights into the genetic architecture of congenital heart disease from animal modeling. Zool Res 2023; 44:577-590. [PMID: 37147909 PMCID: PMC10236297 DOI: 10.24272/j.issn.2095-8137.2022.463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/28/2023] [Indexed: 05/07/2023] Open
Abstract
Congenital heart disease (CHD) is observed in up to 1% of live births and is one of the leading causes of mortality from birth defects. While hundreds of genes have been implicated in the genetic etiology of CHD, their role in CHD pathogenesis is still poorly understood. This is largely a reflection of the sporadic nature of CHD, as well as its variable expressivity and incomplete penetrance. We reviewed the monogenic causes and evidence for oligogenic etiology of CHD, as well as the role of de novo mutations, common variants, and genetic modifiers. For further mechanistic insight, we leveraged single-cell data across species to investigate the cellular expression characteristics of genes implicated in CHD in developing human and mouse embryonic hearts. Understanding the genetic etiology of CHD may enable the application of precision medicine and prenatal diagnosis, thereby facilitating early intervention to improve outcomes for patients with CHD.
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Affiliation(s)
- Wenjuan Zhu
- Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology-Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15201 USA. E-mail:
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Mamasoula C, Bigirumurame T, Chadwick T, Addor MC, Cavero-Carbonell C, Dias CM, Echevarría-González-de-Garibay LJ, Gatt M, Khoshnood B, Klungsoyr K, Randall K, Stoianova S, Haeusler M, Nelen V, Neville AJ, Perthus I, Pierini A, Bertaut-Nativel B, Rissmann A, Rouget F, Schaub B, Tucker D, Wellesley D, Zymak-Zakutnia N, Barisic I, de Walle HEK, Lanzoni M, Sayers G, Mullaney C, Pennington L, Rankin J. Maternal age and the prevalence of congenital heart defects in Europe, 1995-2015: A register-based study. Birth Defects Res 2023; 115:583-594. [PMID: 36734416 DOI: 10.1002/bdr2.2152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/18/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023]
Abstract
BACKGROUND Evidence on the direction and strength of association between maternal age and the prevalence of congenital heart defects (CHD) in different age group categories is conflicting. Some studies have illustrated different trends with an increase in prevalence in younger and older age groups while other studies have reported a linear relationship. Given the increase in maternal age over recent years, it is important to study the CHD prevalence by maternal age. OBJECTIVES To examine the association between maternal age and the prevalence of CHD in Europe between 1995 and 2015 using population-based data from 24 registries belonging to the European Surveillance of Congenital Anomalies (EUROCAT) network. METHODS Associations over time of all nonsyndromic CHD according to maternal age category and for three CHD severity groupings (severity group I: very severe; severity group II: severe; severity group III: less severe) were examined using Bayesian multilevel Poisson regression modeling. Further subgroup analyses were undertaken within four maternal age-bands: ≤24, 25-29, 30-34 and 35-44 years. Descriptive summaries are also presented. RESULTS There were 51,608 nonsyndromic CHD cases in Europe over the 20-year study period. Total prevalence for all CHD combined was increased for younger mothers (≤24 years) and for mothers 35-44 years of age when compared with mothers aged 25-29 years (reference group) (IRR: 1.05, 95% CI: 1.02, 1.07). The total prevalence was increased for severity group I (very severe) only for younger mothers compared to those aged 25-29 years (IRR: 1.14, 95% CI: 1.04, 1.23). We found an increased prevalence of the following CHD subtypes: double outlet right ventricle (IRR:1.33, 95% CI: 1.09, 1.60), hypoplastic left heart syndrome (IRR: 1.18, 95% CI: 1.05, 1.32), hypoplastic right heart syndrome (IRR: 1.41, 95% CI: 1.05, 1.84), atrioventricular septal defect (IRR: 1.15, 95% CI: 1.01, 1.32), coarctation of aorta (IRR: 1.15, 95% CI: 1.03, 1.28) and atrial septal defect (IRR: 1.08, 95% CI: 1.02, 1.13). For older mothers (35-44 years) compared to the reference category, we observed an increased risk in the prevalence for severity group II (IRR: 1.09, 95% CI: 1.03, 1.14), severity group III (IRR: 1.05, 95% CI: 1.01, 1.08) and an increased prevalence of the CHD subtypes: Pulmonary valve stenosis (IRR: 1.22, 95% CI: 1.09, 1.34), ASD (IRR: 1.07, 95% CI: 1.02, 1.13), CoA (IRR: 1.18, 95% CI: 1.06, 1.32) and Tetralogy of Fallot (IRR: 1.14, 95% CI: 1.01, 1.28). Finally, for all age categories compared to the reference category, different associations of ASD and an increased prevalence of CoA was also observed. CONCLUSIONS Based on data for cases of CHD from 24 European population-based registries, evidence of a positive association between maternal age and the total prevalence of CHD for younger (≤24 years old) and older (35-44 years old) mothers was observed. The results suggest that young maternal age (≤24 years old) is a factor associated with severe CHD phenotypes while a positive association between advanced maternal age (35-44 years old) and mild CHD phenotypes was observed.
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Affiliation(s)
| | | | - Thomas Chadwick
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
| | - Marie-Claude Addor
- Department of Woman-Mother-Child, University Medical Center CHUV, Lausanne, Switzerland
| | - Clara Cavero-Carbonell
- Rare Diseases Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, Valencia, Spain
| | - Carlos M Dias
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
- Epidemiology Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Luis-Javier Echevarría-González-de-Garibay
- Ministry of Health of the Basque Government. Directorate for Healthcare Planning, Organisation and Evaluation, Registries and Health Information Unit, Vitoria-Gasteiz, Spain
| | - Miriam Gatt
- Malta Congenital Anomalies Register, Directorate for Health Information and Research, Pietà, Malta
| | - Babak Khoshnood
- Université de Paris, INSERM U1153, CRESS, Obstetrical Perinatal and Pediatric Epidemiology Research Team (EPOPé), Paris, France
| | - Kari Klungsoyr
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Division for Mental and Physical Health, Norwegian Institute of Public Health, Bergen, Norway
| | - Kay Randall
- National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sylvia Stoianova
- South West Congenital Anomaly Register, Bristol Medical School, University of Bristol, Bristol, UK
| | - Martin Haeusler
- Styrian Malformation Registry, Med. University of Graz, Graz, Austria
| | - Vera Nelen
- Provinciaal Instituut voor Hygiene (PIH), Antwerp, Belgium
| | - Amanda J Neville
- Registro IMER - IMER Registry (Emilia Romagna Registry of Birth Defects), Center for Clinical and Epidemiological Research, University of Ferrara, Ferrara, Italy
| | - Isabelle Perthus
- Auvergne registry of congenital anomalies (CEMC-Auvergne), Department of clinical genetics, Centre de Référence des Maladies Rares, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Anna Pierini
- Tuscany Registry of Congenital Defects (RTDC), Institute of Clinical Physiology - National Research Council/ Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | | | - Anke Rissmann
- Malformation Monitoring Centre Saxony-Anhalt, Medical Faculty Otto-von-Guericke University, Magdeburg, Germany
| | - Florence Rouget
- Brittany Registry of Congenital Anomalies, CHU Rennes, University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Bruno Schaub
- French West Indies Registry, Registre des Malformations des Antilles (REMALAN), Maison de la Femme de la Mère et de l'Enfant, University Hospital of Martinique, Fort-de-France, France
| | - David Tucker
- CARIS, Public Health Wales, Singleton Hospital, Swansea, UK
| | - Diana Wellesley
- Wessex Clinical Genetics Department, Princess Anne Hospital, Southampton, UK
| | - Natalya Zymak-Zakutnia
- OMNI-Net Ukraine Birth Defects Program and Khmelnytsky City Children's Hospital, Khmelnytsky, Ukraine
| | - Ingeborg Barisic
- Centre of Excellence for Reproductive and Regenerative Medicine, Children's Hospital Zagreb, Medical School University of Zagreb, Zagreb, Croatia
| | - Hermien E K de Walle
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Monica Lanzoni
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Gerardine Sayers
- Health Service Executive, Dr Steeven's Hospital, Dublin, Ireland
| | - Carmel Mullaney
- Department of Public Health, Service Executive (HSE) South East Area, Limerick, Ireland
| | - Lindsay Pennington
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
| | - Judith Rankin
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
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Webber DM, Li M, MacLeod SL, Tang X, Levy JW, Karim MA, Erickson SW, Hobbs CA. Gene-Folic Acid Interactions and Risk of Conotruncal Heart Defects: Results from the National Birth Defects Prevention Study. Genes (Basel) 2023; 14:genes14010180. [PMID: 36672920 PMCID: PMC9859210 DOI: 10.3390/genes14010180] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Conotruncal heart defects (CTDs) are heart malformations that affect the cardiac outflow tract and typically cause significant morbidity and mortality. Evidence from epidemiological studies suggests that maternal folate intake is associated with a reduced risk of heart defects, including CTD. However, it is unclear if folate-related gene variants and maternal folate intake have an interactive effect on the risk of CTDs. In this study, we performed targeted sequencing of folate-related genes on DNA from 436 case families with CTDs who are enrolled in the National Birth Defects Prevention Study and then tested for common and rare variants associated with CTD. We identified risk alleles in maternal MTHFS (ORmeta = 1.34; 95% CI 1.07 to 1.67), maternal NOS2 (ORmeta = 1.34; 95% CI 1.05 to 1.72), fetal MTHFS (ORmeta = 1.35; 95% CI 1.09 to 1.66), and fetal TCN2 (ORmeta = 1.38; 95% CI 1.12 to 1.70) that are associated with an increased risk of CTD among cases without folic acid supplementation. We detected putative de novo mutations in genes from the folate, homocysteine, and transsulfuration pathways and identified a significant association between rare variants in MGST1 and CTD risk. Results suggest that periconceptional folic acid supplementation is associated with decreased risk of CTD among individuals with susceptible genotypes.
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Affiliation(s)
- Daniel M. Webber
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University at Bloomington, Bloomington, IN 47405, USA
| | - Stewart L. MacLeod
- Division of Birth Defects Research, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xinyu Tang
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Joseph W. Levy
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA
| | - Mohammad A. Karim
- Department of Child Health, College of Medicine, University of Arizona, Phoenix, AZ 85004, USA
- Department of Neurology, Sections on Neurodevelopmental Disorders, Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
| | - Stephen W. Erickson
- Center for Genomics in Public Health and Medicine, RTI International, Research Triangle Park, NC 27709, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123, USA
- Correspondence:
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He GW, Maslen CL, Chen HX, Hou HT, Bai XY, Wang XL, Liu XC, Lu WL, Chen XX, Chen WD, Xing QS, Wu Q, Wang J, Yang Q. Identification of Novel Rare Copy Number Variants Associated with Sporadic Tetralogy of Fallot and Clinical Implications. Clin Genet 2022; 102:391-403. [PMID: 35882632 DOI: 10.1111/cge.14201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. Highly penetrant copy number variants (CNVs) and genes related to the etiology of TOF likely exist with differences among populations. We aimed to identify CNV contributions to sporadic TOF cases in Han Chinese. Genomic DNA was extracted from peripheral blood in 605 subjects (303 sporadic TOF and 302 unaffected Han Chinese [Control] from cardiac centers in China and analyzed by genome-wide association study (GWAS). The GWAS results were compared to existing Database of Genetic Variants. These CNVs were further validated by qPCR. Bioinformatics analyses were performed with Protein-Protein Interaction (PPI) network and KEGG pathway enrichment. Across all chromosomes 119 novel "TOF-specific CNVs" were identified with prevalence of CNVs of 21.5% in chromosomes 1-20 and 37.0% including Chr21/22. In chromosomes 1-20, CNVs on 11q25 (encompasses genes ACAD8, B3GAT1, GLB1L2, GLB1L3, IGSF9B, JAM3, LOC100128239, LOC283177, MIR4697, MIR4697HG, NCAPD3, OPCML, SPATA19, THYN1, and VPS26B) and 14q32.33 (encompasses genes THYN1, OPCML, and NCAPD3) encompass genes most likely to be associated with TOF. Specific CNVs found on the chromosome 21 (6.3%) and 22(11.9%) were also identified in details. PPI network analysis identified the genes covering the specific CNVs related to TOF and the signaling pathways. This study for first time identified novel TOF-specific CNVs in the Han Chinese with higher frequency than in Caucasians and with 11q25 and 14q32.33 not reported in TOF of Caucasians. These novel CNVs identify new candidate genes for TOF and provide new insights into genetic basis of TOF.
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Affiliation(s)
- Guo-Wei He
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China.,Department of Surgery, Oregon Health and Science University, Portland, Oregon, USA
| | - Cheryl L Maslen
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Huan-Xin Chen
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Hai-Tao Hou
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiao-Yan Bai
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiu-Li Wang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiao-Cheng Liu
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Wan-Li Lu
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xin-Xin Chen
- Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei-Dan Chen
- Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Quan-Sheng Xing
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Qin Wu
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Jun Wang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Qin Yang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
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10
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Škorić-Milosavljević D, Tadros R, Bosada FM, Tessadori F, van Weerd JH, Woudstra OI, Tjong FV, Lahrouchi N, Bajolle F, Cordell HJ, Agopian A, Blue GM, Barge-Schaapveld DQ, Gewillig M, Preuss C, Lodder EM, Barnett P, Ilgun A, Beekman L, van Duijvenboden K, Bokenkamp R, Müller-Nurasyid M, Vliegen HW, Konings TC, van Melle JP, van Dijk AP, van Kimmenade RR, Roos-Hesselink JW, Sieswerda GT, Meijboom F, Abdul-Khaliq H, Berger F, Dittrich S, Hitz MP, Moosmann J, Riede FT, Schubert S, Galan P, Lathrop M, Munter HM, Al-Chalabi A, Shaw CE, Shaw PJ, Morrison KE, Veldink JH, van den Berg LH, Evans S, Nobrega MA, Aneas I, Radivojkov-Blagojević M, Meitinger T, Oechslin E, Mondal T, Bergin L, Smythe JF, Altamirano-Diaz L, Lougheed J, Bouma BJ, Chaix MA, Kline J, Bassett AS, Andelfinger G, van der Palen RL, Bouvagnet P, Clur SAB, Breckpot J, Kerstjens-Frederikse WS, Winlaw DS, Bauer UM, Mital S, Goldmuntz E, Keavney B, Bonnet D, Mulder BJ, Tanck MW, Bakkers J, Christoffels VM, Boogerd CJ, Postma AV, Bezzina CR. Common Genetic Variants Contribute to Risk of Transposition of the Great Arteries. Circ Res 2022; 130:166-180. [PMID: 34886679 PMCID: PMC8768504 DOI: 10.1161/circresaha.120.317107] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
Abstract
RATIONALE Dextro-transposition of the great arteries (D-TGA) is a severe congenital heart defect which affects approximately 1 in 4,000 live births. While there are several reports of D-TGA patients with rare variants in individual genes, the majority of D-TGA cases remain genetically elusive. Familial recurrence patterns and the observation that most cases with D-TGA are sporadic suggest a polygenic inheritance for the disorder, yet this remains unexplored. OBJECTIVE We sought to study the role of common single nucleotide polymorphisms (SNPs) in risk for D-TGA. METHODS AND RESULTS We conducted a genome-wide association study in an international set of 1,237 patients with D-TGA and identified a genome-wide significant susceptibility locus on chromosome 3p14.3, which was subsequently replicated in an independent case-control set (rs56219800, meta-analysis P=8.6x10-10, OR=0.69 per C allele). SNP-based heritability analysis showed that 25% of variance in susceptibility to D-TGA may be explained by common variants. A genome-wide polygenic risk score derived from the discovery set was significantly associated to D-TGA in the replication set (P=4x10-5). The genome-wide significant locus (3p14.3) co-localizes with a putative regulatory element that interacts with the promoter of WNT5A, which encodes the Wnt Family Member 5A protein known for its role in cardiac development in mice. We show that this element drives reporter gene activity in the developing heart of mice and zebrafish and is bound by the developmental transcription factor TBX20. We further demonstrate that TBX20 attenuates Wnt5a expression levels in the developing mouse heart. CONCLUSIONS This work provides support for a polygenic architecture in D-TGA and identifies a susceptibility locus on chromosome 3p14.3 near WNT5A. Genomic and functional data support a causal role of WNT5A at the locus.
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Affiliation(s)
- Doris Škorić-Milosavljević
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
| | - Rafik Tadros
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada (R.T., M.-A.C.)
| | - Fernanda M. Bosada
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
| | - Jan Hendrik van Weerd
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Odilia I. Woudstra
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Fleur V.Y. Tjong
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Fanny Bajolle
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Germany (F.B., S.S.)
| | - Heather J. Cordell
- Population Health Sciences Institute, Newcastle University, Newcastle, United Kingdom (H.J.C.)
| | - A.J. Agopian
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, TX (A.J.A.)
| | - Gillian M. Blue
- Heart Centre for Children, The Children’s Hospital at Westmead and Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Australia (G.M.B., D.S.W.)
| | | | | | - Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Québec, Canada (C.P., G.A.)
- The Jackson Laboratory, Bar Harbor, ME (C.P.)
| | - Elisabeth M. Lodder
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
| | - Phil Barnett
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Leander Beekman
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Regina Bokenkamp
- Division of Pediatric Cardiology, Department of Pediatrics (R.B., R.L.F.v.d.P.), Leiden University Medical Center, The Netherlands
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany (M.M.-N.)
- IBE, Faculty of Medicine, LMU Munich, Germany (M.M.-N.)
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany (M.M.-N.)
| | - Hubert W. Vliegen
- Department of Cardiology (H.W.V.), Leiden University Medical Center, The Netherlands
| | - Thelma C. Konings
- Department of Cardiology, Amsterdam University Medical Centers, VU Amsterdam, The Netherlands (T.C.K.)
| | - Joost P. van Melle
- Department of Cardiology, University Medical Center Groningen, University of Groningen, The Netherlands (J.P.v.M.)
| | - Arie P.J. van Dijk
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands (A.P.J.v.D., R.R.J.v.K.)
| | - Roland R.J. van Kimmenade
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands (A.P.J.v.D., R.R.J.v.K.)
- Department of Cardiology, Maastricht University Medical Center, The Netherlands (R.R.J.v.K.)
| | - Jolien W. Roos-Hesselink
- Department of Cardiology, Erasmus Medical Center, Erasmus University, Rotterdam, The Netherlands (J.W.R.-H.)
| | - Gertjan T. Sieswerda
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Folkert Meijboom
- Department of Cardiology, University Medical Center Utrecht, The Netherlands (O.I.W., G.T.S., F.M.)
| | - Hashim Abdul-Khaliq
- Saarland University Medical Center, Department of Pediatric Cardiology, Homburg, Germany (H.A.-K.)
| | - Felix Berger
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de référence Malformations Cardiaques Congénitales Complexes - M3C, Hôpital Necker Enfants Malades, APHP and Université Paris Descartes, Sorbonne Paris Cité, Paris, France (F.B., D.B.)
- Charité, Universitätsmedizin Berlin, Department for Paediatric Cardiology, Germany (F.B.)
| | - Sven Dittrich
- Department of Pediatric Cardiology, Friedrich-Alexander-University of Erlangen-Nuernberg (FAU), Germany (S.D., J.M.)
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein/Campus Kiel, DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Germany (M.-P.H.)
- Department of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany (M.-P.H.)
| | - Julia Moosmann
- Department of Pediatric Cardiology, Friedrich-Alexander-University of Erlangen-Nuernberg (FAU), Germany (S.D., J.M.)
| | - Frank-Thomas Riede
- Leipzig Heart Center, Department of Pediatric Cardiology, University of Leipzig, Germany (F.-T.R.)
| | - Stephan Schubert
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Germany (F.B., S.S.)
- Heart and Diabetes Center NRW, Center of Congenital Heart Disease, Ruhr-University of Bochum, Bad Oeynhausen, Germany (S.S.)
| | - Pilar Galan
- Sorbonne Paris Nord (Paris 13) University, Inserm U1153, Inrae U1125, Cnam, Nutritional Epidemiology Research Team (EREN), Epidemiology and Statistics Research Center – University of Paris (CRESS), Bobigny, France (P.G.)
| | - Mark Lathrop
- McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Québec, Canada (M.L., H.M.M.)
| | - Hans M. Munter
- McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Québec, Canada (M.L., H.M.M.)
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King’s College London, United Kingdom (A.A.-C.)
| | - Christopher E. Shaw
- United Kingdom Dementia Research Institute Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, United Kingdom (C.E.S.)
- Centre for Brain Research, University of Auckland, New Zealand (C.E.S.)
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield and NIHR Sheffield Biomedical Research Centre for Translational Neuroscience, United Kingdom (P.J.S.)
| | - Karen E. Morrison
- Faculty of Medicine Health & Life Sciences, Queens University Belfast, United Kingdom (K.E.M.)
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands (J.H.V., L.H.v.d.B.)
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands (J.H.V., L.H.v.d.B.)
| | - Sylvia Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (S.E.)
| | | | - Ivy Aneas
- Department of Human Genetics, University of Chicago, IL (M.A.N., I.A.)
| | | | - Thomas Meitinger
- Helmholtz Zentrum Munich, Institut of Human Genetics, Neuherberg, Germany (M.R.-B., T.M.)
- Division of Cardiology, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada (T.M.)
| | - Erwin Oechslin
- Peter Munk Cardiac Center, Toronto Congenital Cardiac Centre for Adults and University of Toronto, Canada (E.O.)
| | - Tapas Mondal
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Germany (T.M.)
| | - Lynn Bergin
- Division of Cardiology, Department of Medicine, London Health Sciences Centre, ON, Canada (L.B.)
| | - John F. Smythe
- Division of Cardiology, Department of Pediatrics, Kingston General Hospital, ON, Canada (J.F.S.)
| | | | - Jane Lougheed
- Division of Cardiology, Department of Pediatrics, Children’s Hospital of Eastern Ontario, Ottawa, Canada (J.L.)
| | - Berto J. Bouma
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Marie-A. Chaix
- Department of Medicine, Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, Québec, Canada (R.T., M.-A.C.)
| | - Jennie Kline
- Department of Epidemiology, Mailman School of Public Health, Columbia University, NY (J.K.)
| | - Anne S. Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health (A.S.B.)
- Department of Psychiatry, University of Toronto, Toronto General Hospital, University Health Network, Ontario, Canada (A.S.B.)
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Québec, Canada (C.P., G.A.)
| | - Roel L.F. van der Palen
- Division of Pediatric Cardiology, Department of Pediatrics (R.B., R.L.F.v.d.P.), Leiden University Medical Center, The Netherlands
| | - Patrice Bouvagnet
- CPDPN, Hôpital MFME, CHU Martinique, Fort de France, Martinique, France (P.B.)
| | - Sally-Ann B. Clur
- Department of Pediatric Cardiology, Emma Children’s Hospital Amsterdam University Medical Centers (AMC), The Netherlands (S.-A.B.C.)
- Centre for Congenital Heart Disease Amsterdam-Leiden (CAHAL) (S.-A.B.C.)
| | - Jeroen Breckpot
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
- Center for Human Genetics University Hospitals KU Leuven, Belgium (J.B.)
| | | | - David S. Winlaw
- Heart Centre for Children, The Children’s Hospital at Westmead and Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Australia (G.M.B., D.S.W.)
| | - Ulrike M.M. Bauer
- National Register for Congenital Heart Defects, DZHK (German Centre for Cardiovascular Research), Berlin, Germany (U.M.M.B.)
| | - Seema Mital
- Hospital for Sick Children, University of Toronto, Ontario, Canada (S.M.)
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (E.G.)
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom (B.K.)
| | - Damien Bonnet
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de référence Malformations Cardiaques Congénitales Complexes - M3C, Hôpital Necker Enfants Malades, APHP and Université Paris Descartes, Sorbonne Paris Cité, Paris, France (F.B., D.B.)
| | - Barbara J. Mulder
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
| | - Michael W.T. Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health (APH), Amsterdam University Medical Centers, University of Amsterdam, The Netherlands (M.W.T.T.)
| | - Jeroen Bakkers
- Division of Heart and Lungs, Department of Medical Physiology, University Medical Center Utrecht, the Netherlands (J.B.)
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Cornelis J. Boogerd
- Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (F.T., J.B., C.J.B.)
| | - Alex V. Postma
- Department of Human Genetics, Amsterdam University Medical Centers, The Netherlands (D.S.-M., E.M.L., A.V.P.)
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Cardiovascular Sciences, the Netherlands (F.M.B., J.H.v.W., P.B., A.I., K.v.D., V.M.C., A.V.P.)
| | - Connie R. Bezzina
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, The Netherlands (D.S.-M., R.T., O.I.W., F.V.Y.T., N.L., E.M.L., L.B., B.J.B., B.J.M., C.R.B.)
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11
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Morton SU, Quiat D, Seidman JG, Seidman CE. Genomic frontiers in congenital heart disease. Nat Rev Cardiol 2022; 19:26-42. [PMID: 34272501 PMCID: PMC9236191 DOI: 10.1038/s41569-021-00587-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
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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12
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In vivo identification and validation of novel potential predictors for human cardiovascular diseases. PLoS One 2021; 16:e0261572. [PMID: 34919578 PMCID: PMC8682894 DOI: 10.1371/journal.pone.0261572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022] Open
Abstract
Genetics crucially contributes to cardiovascular diseases (CVDs), the global leading cause of death. Since the majority of CVDs can be prevented by early intervention there is a high demand for the identification of predictive causative genes. While genome wide association studies (GWAS) correlate genes and CVDs after diagnosis and provide a valuable resource for such causative candidate genes, often preferentially those with previously known or suspected function are addressed further. To tackle the unaddressed blind spot of understudied genes, we particularly focused on the validation of human heart phenotype-associated GWAS candidates with little or no apparent connection to cardiac function. Building on the conservation of basic heart function and underlying genetics from fish to human we combined CRISPR/Cas9 genome editing of the orthologs of human GWAS candidates in isogenic medaka with automated high-throughput heart rate analysis. Our functional analyses of understudied human candidates uncovered a prominent fraction of heart rate associated genes from adult human patients impacting on the heart rate in embryonic medaka already in the injected generation. Following this pipeline, we identified 16 GWAS candidates with potential diagnostic and predictive power for human CVDs.
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13
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Yang W, Bai J, Song X, Zhang S, Chen N, You T, Yi K, Li Z, Xie D, Xie X. CCN1 gene polymorphisms associated with congenital heart disease susceptibility in Northwest Chinese population from different high-altitude areas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:56927-56937. [PMID: 34080118 DOI: 10.1007/s11356-021-14428-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
High-altitude hypoxic environment exposure is considered one of the risk factors for congenital heart disease (CHD), but the genetic factors involved are still unclear. CCN1, one of the synergistic molecules in the hypoxic response, is also an indispensable molecule in cardiac development. Considering that CCN1 may play an important role in the occurrence of CHD in high-altitude areas, we investigated the association between CCN1 polymorphisms and CHD susceptibility in Northwest Chinese population from different high-altitude areas. We conducted a case-control study with a total of 395 CHD cases and 486 controls to evaluate the associations of CCN1 polymorphisms with CHD risk. Our results showed that the protective alleles rs3753793-C (OR = 0.59, 95% CI = 0.42-0.81, P = 0.001), rs2297141-A (OR = 0.66, 95% CI = 0.49-0.90, P = 0.001), and C-A haplotype of rs3753793-rs2297141 (OR = 0.58, 95% CI = 0.42-0.82, P = 0.002) were significantly associated with a decreased atrial septal defect (ASD) risk. Further subgroup analysis in different geography populations revealed robust association of SNP rs2297141 with ASD risk in a Han population residing in high altitude of 2500-4287 m. We also found that the frequency of protective alleles was higher in high-altitude population, and the alleles were responsible for the difference of oxygen physiology-related erythrocyte parameters in different high-altitude populations. rs3753793-C and rs2297141-A are likely related to high altitude and hypoxia adaptation, which may also be the reason for the association between CCN1 polymorphism and ASD risk.
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Affiliation(s)
- Wenke Yang
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
- Gansu Cardiovascular Institute, People's Hospital of Lanzhou City, Lanzhou, China
| | - Jun Bai
- Department of Hematology, Gansu Provincial Key Laboratory of Hematology, Second Hospital of Lanzhou University, Lanzhou, China
| | - Xinyu Song
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Shasha Zhang
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Nana Chen
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Tao You
- Department of Cardiac Surgery, Gansu Provincial Hospital, Lanzhou, China
| | - Kang Yi
- Department of Cardiac Surgery, Gansu Provincial Hospital, Lanzhou, China
| | - Zhenglin Li
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Dingxiong Xie
- Gansu Cardiovascular Institute, People's Hospital of Lanzhou City, Lanzhou, China
| | - Xiaodong Xie
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.
- Gansu Cardiovascular Institute, People's Hospital of Lanzhou City, Lanzhou, China.
- Genetics Medicine Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China.
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14
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Reuter MS, Chaturvedi RR, Jobling RK, Pellecchia G, Hamdan O, Sung WW, Nalpathamkalam T, Attaluri P, Silversides CK, Wald RM, Marshall CR, Williams S, Keavney BD, Thiruvahindrapuram B, Scherer SW, Bassett AS. Clinical Genetic Risk Variants Inform a Functional Protein Interaction Network for Tetralogy of Fallot. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2021; 14:e003410. [PMID: 34328347 PMCID: PMC8373675 DOI: 10.1161/circgen.121.003410] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Tetralogy of Fallot (TOF)-the most common cyanotic heart defect in newborns-has evidence of multiple genetic contributing factors. Identifying variants that are clinically relevant is essential to understand patient-specific disease susceptibility and outcomes and could contribute to delineating pathomechanisms. METHODS Using a clinically driven strategy, we reanalyzed exome sequencing data from 811 probands with TOF, to identify rare loss-of-function and other likely pathogenic variants in genes associated with congenital heart disease. RESULTS We confirmed a major contribution of likely pathogenic variants in FLT4 (VEGFR3 [vascular endothelial growth factor receptor 3]; n=14) and NOTCH1 (n=10) and identified 1 to 3 variants in each of 21 other genes, including ATRX, DLL4, EP300, GATA6, JAG1, NF1, PIK3CA, RAF1, RASA1, SMAD2, and TBX1. In addition, multiple loss-of-function variants provided support for 3 emerging congenital heart disease/TOF candidate genes: KDR (n=4), IQGAP1 (n=3), and GDF1 (n=8). In total, these variants were identified in 63 probands (7.8%). Using the 26 composite genes in a STRING protein interaction enrichment analysis revealed a biologically relevant network (P=3.3×10-16), with VEGFR2 (vascular endothelial growth factor receptor 2; KDR) and NOTCH1 (neurogenic locus notch homolog protein 1) representing central nodes. Variants associated with arrhythmias/sudden death and heart failure indicated factors that could influence long-term outcomes. CONCLUSIONS The results are relevant to precision medicine for TOF. They suggest considerable clinical yield from genome-wide sequencing, with further evidence for KDR (VEGFR2) as a congenital heart disease/TOF gene and for VEGF (vascular endothelial growth factor) and Notch signaling as mechanisms in human disease. Harnessing the genetic heterogeneity of single gene defects could inform etiopathogenesis and help prioritize novel candidate genes for TOF.
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Affiliation(s)
- Miriam S. Reuter
- CGEn, Univ Health Network, Toronto, ON, Canada
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
- Program in Genetics & Genome Biology, Univ Health Network, Toronto, ON, Canada
| | - Rajiv R. Chaturvedi
- Labatt Family Heart Ctr, Univ Health Network, Toronto, ON, Canada
- Ontario Fetal Ctr, Mt Sinai Hospital, Univ Health Network, Toronto, ON, Canada
- Ted Rogers Ctr for Heart Rsrch, Cardiac Genome Clinic, Univ Health Network, Toronto, ON, Canada
| | - Rebekah K. Jobling
- Ted Rogers Ctr for Heart Rsrch, Cardiac Genome Clinic, Univ Health Network, Toronto, ON, Canada
- Division of Clinical & Metabolic Genetics, Univ Health Network, Toronto, ON, Canada
- Genome Diagnostics, Dept of Paediatric Laboratory Medicine, The Hospital for Sick Children, Univ Health Network, Toronto, ON, Canada
| | | | - Omar Hamdan
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
| | - Wilson W.L. Sung
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
| | | | - Pratyusha Attaluri
- Medical Genomics Program, Dept of Molecular Genetics, Univ Health Network, Toronto, ON, Canada
| | - Candice K. Silversides
- Division of Cardiology, Toronto Congenital Cardiac Ctr for Adults at the Peter Munk Cardiac Ctr, Dept of Medicine, Univ Health Network, Toronto, ON, Canada
| | - Rachel M. Wald
- Labatt Family Heart Ctr, Univ Health Network, Toronto, ON, Canada
- Division of Cardiology, Toronto Congenital Cardiac Ctr for Adults at the Peter Munk Cardiac Ctr, Dept of Medicine, Univ Health Network, Toronto, ON, Canada
| | - Christian R. Marshall
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
- Genome Diagnostics, Dept of Paediatric Laboratory Medicine, The Hospital for Sick Children, Univ Health Network, Toronto, ON, Canada
- Laboratory Medicine & Pathobiology, Univ Health Network, Toronto, ON, Canada
| | - Simon Williams
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine & Health, The Univ of Manchester, Manchester, UK
- Manchester Univ NHS Foundation Trust, Manchester Academic Health Science Ctr, Manchester, UK
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine & Health, The Univ of Manchester, Manchester, UK
- Manchester Univ NHS Foundation Trust, Manchester Academic Health Science Ctr, Manchester, UK
| | | | - Stephen W. Scherer
- The Ctr for Applied Genomics, Univ Health Network, Toronto, ON, Canada
- Program in Genetics & Genome Biology, Univ Health Network, Toronto, ON, Canada
- Dept of Molecular Genetics, Univ Health Network, Toronto, ON, Canada
- McLaughlin Ctr, Univ Health Network, Toronto, ON, Canada
| | - Anne S. Bassett
- Division of Cardiology, Toronto Congenital Cardiac Ctr for Adults at the Peter Munk Cardiac Ctr, Dept of Medicine, Univ Health Network, Toronto, ON, Canada
- Clinical Genetics Research Program, Ctr for Addiction & Mental Health, Toronto, ON, Canada
- The Dalglish Family 22q Clinic for Adults with 22q11.2 Deletion Syndrome, Dept of Psychiatry & Toronto General Rsrch Inst, Univ Health Network, Toronto, ON, Canada
- Dept of Psychiatry, Univ of Toronto, Univ Health Network, Toronto, ON, Canada
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15
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Dyer LA, Rugonyi S. Fetal Blood Flow and Genetic Mutations in Conotruncal Congenital Heart Disease. J Cardiovasc Dev Dis 2021; 8:90. [PMID: 34436232 PMCID: PMC8397097 DOI: 10.3390/jcdd8080090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/19/2022] Open
Abstract
In congenital heart disease, the presence of structural defects affects blood flow in the heart and circulation. However, because the fetal circulation bypasses the lungs, fetuses with cyanotic heart defects can survive in utero but need prompt intervention to survive after birth. Tetralogy of Fallot and persistent truncus arteriosus are two of the most significant conotruncal heart defects. In both defects, blood access to the lungs is restricted or non-existent, and babies with these critical conditions need intervention right after birth. While there are known genetic mutations that lead to these critical heart defects, early perturbations in blood flow can independently lead to critical heart defects. In this paper, we start by comparing the fetal circulation with the neonatal and adult circulation, and reviewing how altered fetal blood flow can be used as a diagnostic tool to plan interventions. We then look at known factors that lead to tetralogy of Fallot and persistent truncus arteriosus: namely early perturbations in blood flow and mutations within VEGF-related pathways. The interplay between physical and genetic factors means that any one alteration can cause significant disruptions during development and underscore our need to better understand the effects of both blood flow and flow-responsive genes.
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Affiliation(s)
- Laura A. Dyer
- Department of Biology, University of Portland, Portland, OR 97203, USA;
| | - Sandra Rugonyi
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
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16
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Diab NS, Barish S, Dong W, Zhao S, Allington G, Yu X, Kahle KT, Brueckner M, Jin SC. Molecular Genetics and Complex Inheritance of Congenital Heart Disease. Genes (Basel) 2021; 12:1020. [PMID: 34209044 PMCID: PMC8307500 DOI: 10.3390/genes12071020] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/09/2023] Open
Abstract
Congenital heart disease (CHD) is the most common congenital malformation and the leading cause of mortality therein. Genetic etiologies contribute to an estimated 90% of CHD cases, but so far, a molecular diagnosis remains unsolved in up to 55% of patients. Copy number variations and aneuploidy account for ~23% of cases overall, and high-throughput genomic technologies have revealed additional types of genetic variation in CHD. The first CHD risk genotypes identified through high-throughput sequencing were de novo mutations, many of which occur in chromatin modifying genes. Murine models of cardiogenesis further support the damaging nature of chromatin modifying CHD mutations. Transmitted mutations have also been identified through sequencing of population scale CHD cohorts, and many transmitted mutations are enriched in cilia genes and Notch or VEGF pathway genes. While we have come a long way in identifying the causes of CHD, more work is required to end the diagnostic odyssey for all CHD families. Complex genetic explanations of CHD are emerging but will require increasingly sophisticated analysis strategies applied to very large CHD cohorts before they can come to fruition in providing molecular diagnoses to genetically unsolved patients. In this review, we discuss the genetic architecture of CHD and biological pathways involved in its pathogenesis.
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Affiliation(s)
- Nicholas S. Diab
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Syndi Barish
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Shujuan Zhao
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
| | - Garrett Allington
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Xiaobing Yu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Kristopher T. Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sheng Chih Jin
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Pediatrics, School of Medicine, Washington University, St. Louis, MO 63110, USA
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17
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From Stem Cells to Populations-Using hiPSC, Next-Generation Sequencing, and GWAS to Explore the Genetic and Molecular Mechanisms of Congenital Heart Defects. Genes (Basel) 2021; 12:genes12060921. [PMID: 34208537 PMCID: PMC8235101 DOI: 10.3390/genes12060921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/01/2021] [Accepted: 06/12/2021] [Indexed: 01/16/2023] Open
Abstract
Congenital heart defects (CHD) are developmental malformations affecting the heart and the great vessels. Early heart development requires temporally regulated crosstalk between multiple cell types, signaling pathways, and mechanical forces of early blood flow. While both genetic and environmental factors have been recognized to be involved, identifying causal genes in non-syndromic CHD has been difficult. While variants following Mendelian inheritance have been identified by linkage analysis in a few families with multiple affected members, the inheritance pattern in most familial cases is complex, with reduced penetrance and variable expressivity. Furthermore, most non-syndromic CHD are sporadic. Improved sequencing technologies and large biobank collections have enabled genome-wide association studies (GWAS) in non-syndromic CHD. The ability to generate human to create human induced pluripotent stem cells (hiPSC) and further differentiate them to organotypic cells enables further exploration of genotype–phenotype correlations in patient-derived cells. Here we review how these technologies can be used in unraveling the genetics and molecular mechanisms of heart development.
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18
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Li M, Lyu C, Huang M, Do C, Tycko B, Lupo PJ, MacLeod SL, Randolph CE, Liu N, Witte JS, Hobbs CA. Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease. BMC Genom Data 2021; 22:20. [PMID: 34112112 PMCID: PMC8194170 DOI: 10.1186/s12863-021-00975-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/02/2021] [Indexed: 12/27/2022] Open
Abstract
Background Most congenital heart defects (CHDs) result from complex interactions among genetic susceptibilities, epigenetic modifications, and maternal environmental exposures. Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation will enhance our understanding of pathogenesis in this important type of congenital disorder. We investigated cis-acting effects of genetic single nucleotide polymorphisms (SNPs) on local DNA methylation patterns within 83 cardiac tissue samples and prioritized their contributions to CHD risk by leveraging results of CHD genome-wide association studies (GWAS) and their effects on cardiac gene expression. Results We identified 13,901 potential methylation quantitative trait loci (mQTLs) with a false discovery threshold of 5%. Further co-localization analyses and Mendelian randomization indicated that genetic variants near the HLA-DRB6 gene on chromosome 6 may contribute to CHD risk by regulating the methylation status of nearby CpG sites. Additional SNPs in genomic regions on chromosome 10 (TNKS2-AS1 gene) and chromosome 14 (LINC01629 gene) may simultaneously influence epigenetic and transcriptomic variations within cardiac tissues. Conclusions Our results support the hypothesis that genetic variants may influence the risk of CHDs through regulating the changes of DNA methylation and gene expression. Our results can serve as an important source of information that can be integrated with other genetic studies of heart diseases, especially CHDs. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00975-2.
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Affiliation(s)
- Ming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA.
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | | | | | | | - Nianjun Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - John S Witte
- University of California at San Francisco, San Francisco, CA, 94158, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
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19
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Kathiriya IS, Rao KS, Iacono G, Devine WP, Blair AP, Hota SK, Lai MH, Garay BI, Thomas R, Gong HZ, Wasson LK, Goyal P, Sukonnik T, Hu KM, Akgun GA, Bernard LD, Akerberg BN, Gu F, Li K, Speir ML, Haeussler M, Pu WT, Stuart JM, Seidman CE, Seidman JG, Heyn H, Bruneau BG. Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease. Dev Cell 2021; 56:292-309.e9. [PMID: 33321106 PMCID: PMC7878434 DOI: 10.1016/j.devcel.2020.11.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 11/18/2020] [Indexed: 01/10/2023]
Abstract
Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways-including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics-in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.
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Affiliation(s)
- Irfan S Kathiriya
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Kavitha S Rao
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Giovanni Iacono
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - W Patrick Devine
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pathology, University of California, San Francisco, CA 94158, USA
| | - Andrew P Blair
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Swetansu K Hota
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Michael H Lai
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Bayardo I Garay
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | | | - Henry Z Gong
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Piyush Goyal
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Tatyana Sukonnik
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Kevin M Hu
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Gunes A Akgun
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Laure D Bernard
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fei Gu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kai Li
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew L Speir
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02115, USA
| | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94158, USA.
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20
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Lin H, McBride KL, Garg V, Zhao MT. Decoding Genetics of Congenital Heart Disease Using Patient-Derived Induced Pluripotent Stem Cells (iPSCs). Front Cell Dev Biol 2021; 9:630069. [PMID: 33585486 PMCID: PMC7873857 DOI: 10.3389/fcell.2021.630069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Congenital heart disease (CHD) is the most common cause of infant death associated with birth defects. Recent next-generation genome sequencing has uncovered novel genetic etiologies of CHD, from inherited and de novo variants to non-coding genetic variants. The next phase of understanding the genetic contributors of CHD will be the functional illustration and validation of this genome sequencing data in cellular and animal model systems. Human induced pluripotent stem cells (iPSCs) have opened up new horizons to investigate genetic mechanisms of CHD using clinically relevant and patient-specific cardiac cells such as cardiomyocytes, endothelial/endocardial cells, cardiac fibroblasts and vascular smooth muscle cells. Using cutting-edge CRISPR/Cas9 genome editing tools, a given genetic variant can be corrected in diseased iPSCs and introduced to healthy iPSCs to define the pathogenicity of the variant and molecular basis of CHD. In this review, we discuss the recent progress in genetics of CHD deciphered by large-scale genome sequencing and explore how genome-edited patient iPSCs are poised to decode the genetic etiologies of CHD by coupling with single-cell genomics and organoid technologies.
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Affiliation(s)
- Hui Lin
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Kim L McBride
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Vidu Garg
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
| | - Ming-Tao Zhao
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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21
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Lahm H, Jia M, Dreßen M, Wirth F, Puluca N, Gilsbach R, Keavney BD, Cleuziou J, Beck N, Bondareva O, Dzilic E, Burri M, König KC, Ziegelmüller JA, Abou-Ajram C, Neb I, Zhang Z, Doppler SA, Mastantuono E, Lichtner P, Eckstein G, Hörer J, Ewert P, Priest JR, Hein L, Lange R, Meitinger T, Cordell HJ, Müller-Myhsok B, Krane M. Congenital heart disease risk loci identified by genome-wide association study in European patients. J Clin Invest 2021; 131:141837. [PMID: 33201861 PMCID: PMC7810487 DOI: 10.1172/jci141837] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022] Open
Abstract
Genetic factors undoubtedly affect the development of congenital heart disease (CHD) but still remain ill defined. We sought to identify genetic risk factors associated with CHD and to accomplish a functional analysis of SNP-carrying genes. We performed a genome-wide association study (GWAS) of 4034 White patients with CHD and 8486 healthy controls. One SNP on chromosome 5q22.2 reached genome-wide significance across all CHD phenotypes and was also indicative for septal defects. One region on chromosome 20p12.1 pointing to the MACROD2 locus identified 4 highly significant SNPs in patients with transposition of the great arteries (TGA). Three highly significant risk variants on chromosome 17q21.32 within the GOSR2 locus were detected in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence the expression of WNT3, and the variant rs870142 related to septal defects is proposed to influence the expression of MSX1. We analyzed the expression of all 4 genes during cardiac differentiation of human and murine induced pluripotent stem cells in vitro and by single-cell RNA-Seq analyses of developing murine and human hearts. Our data show that MACROD2, GOSR2, WNT3, and MSX1 play an essential functional role in heart development at the embryonic and newborn stages.
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Affiliation(s)
- Harald Lahm
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Meiwen Jia
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry Munich, Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Felix Wirth
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Nazan Puluca
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Ralf Gilsbach
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site RheinMain, Frankfurt am Main, Germany
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Julie Cleuziou
- Department of Congenital and Paediatric Heart Surgery, German Heart Center Munich, Munich, Germany
| | - Nicole Beck
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Olga Bondareva
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elda Dzilic
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Melchior Burri
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Karl C. König
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Johannes A. Ziegelmüller
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Claudia Abou-Ajram
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Irina Neb
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Zhong Zhang
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Stefanie A. Doppler
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Elisa Mastantuono
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Peter Lichtner
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Gertrud Eckstein
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Jürgen Hörer
- Department of Congenital and Paediatric Heart Surgery, German Heart Center Munich, Munich, Germany
| | - Peter Ewert
- Department of Pediatric Cardiology and Congenital Heart Disease, German Heart Center Munich, Munich, Germany
| | - James R. Priest
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS, Center for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research) — Partner Site Munich Heart Alliance, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research) — Partner Site Munich Heart Alliance, Munich, Germany
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry Munich, Munich, Germany
- Munich Cluster of Systems Biology, SyNergy, Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Markus Krane
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research) — Partner Site Munich Heart Alliance, Munich, Germany
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22
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Ma ACH, Mak CCY, Yeung KS, Pei SLC, Ying D, Yu MHC, Hasan KMM, Chen X, Chow PC, Cheung YF, Chung BHY. Monoallelic Mutations in CC2D1A Suggest a Novel Role in Human Heterotaxy and Ciliary Dysfunction. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 13:e003000. [PMID: 33196317 PMCID: PMC7748040 DOI: 10.1161/circgen.120.003000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Human heterotaxy is a group of congenital disorders characterized by misplacement of one or more organs according to the left-right axis. The genetic causes of human heterotaxy are highly heterogeneous. METHODS We performed exome sequencing in a cohort of 26 probands with heterotaxy followed by gene burden analysis for the enrichment of novel rare damaging mutations. Transcription activator-like effector nuclease was used to generate somatic loss-of-function mutants in a zebrafish model. Ciliary defects were examined by whole-mount immunostaining of acetylated α-tubulin. RESULTS We identified a significant enrichment of novel rare damaging mutations in the CC2D1A gene. Seven occurrences of CC2D1A mutations were found to affect 4 highly conserved amino acid residues of the protein. Functional analyses in the transcription activator-like effector nuclease-mediated zebrafish knockout models were performed, and heterotaxy phenotypes of the cardiovascular and gastrointestinal systems in both somatic and germline mutants were observed. Defective cilia were demonstrated by whole-mount immunostaining of acetylated α-tubulin. These abnormalities were rescued by wild-type cc2d1a mRNA but not cc2d1a mutant mRNA, strongly suggesting a loss-of-function mechanism. On the other hand, overexpression of cc2d1a orthologous mutations cc2d1a P559L and cc2d1a G808V (orthologous to human CC2D1A P532L and CC2D1A G781V) did not affect embryonic development. CONCLUSIONS Using a zebrafish model, we were able to establish a novel association of CC2D1A with heterotaxy and ciliary dysfunction in the F2 generation via a loss-of-function mechanism. Future mechanistic studies are needed for a better understanding of the role of CC2D1A in left-right patterning and ciliary dysfunction.
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Affiliation(s)
- Alvin Chun Hang Ma
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrate Region, China (A.C.H., K.M.M.H.)
| | - Christopher Chun Yu Mak
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
| | - Kit San Yeung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
| | - Steven Lim Cho Pei
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
| | - Dingge Ying
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
| | - Mullin Ho Chung Yu
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
| | - Kazi Md Mahmudul Hasan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrate Region, China (A.C.H., K.M.M.H.)
| | - Xiangke Chen
- Laboratory of Neurodegenerative Diseases, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China (X.C.)
| | - Pak Cheong Chow
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
| | - Yiu Fai Cheung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
| | - Brian Hon Yin Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Kong Kong, Hong Kong Special Administrate Region, China (C.C.Y.M., K.S.Y., S.L.C.P., D.Y., M.H.C.Y., P.C.C., Y.F.C., B.H.Y.C.)
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23
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Trevino CE, Holleman AM, Corbitt H, Maslen CL, Rosser TC, Cutler DJ, Johnston HR, Rambo-Martin BL, Oberoi J, Dooley KJ, Capone GT, Reeves RH, Cordell HJ, Keavney BD, Agopian AJ, Goldmuntz E, Gruber PJ, O'Brien JE, Bittel DC, Wadhwa L, Cua CL, Moskowitz IP, Mulle JG, Epstein MP, Sherman SL, Zwick ME. Identifying genetic factors that contribute to the increased risk of congenital heart defects in infants with Down syndrome. Sci Rep 2020; 10:18051. [PMID: 33093519 PMCID: PMC7582922 DOI: 10.1038/s41598-020-74650-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/05/2020] [Indexed: 01/16/2023] Open
Abstract
Atrioventricular septal defects (AVSD) are a severe congenital heart defect present in individuals with Down syndrome (DS) at a > 2000-fold increased prevalence compared to the general population. This study aimed to identify risk-associated genes and pathways and to examine a potential polygenic contribution to AVSD in DS. We analyzed a total cohort of 702 individuals with DS with or without AVSD, with genomic data from whole exome sequencing, whole genome sequencing, and/or array-based imputation. We utilized sequence kernel association testing and polygenic risk score (PRS) methods to examine rare and common variants. Our findings suggest that the Notch pathway, particularly NOTCH4, as well as genes involved in the ciliome including CEP290 may play a role in AVSD in DS. These pathways have also been implicated in DS-associated AVSD in prior studies. A polygenic component for AVSD in DS has not been examined previously. Using weights based on the largest genome-wide association study of congenital heart defects available (2594 cases and 5159 controls; all general population samples), we found PRS to be associated with AVSD with odds ratios ranging from 1.2 to 1.3 per standard deviation increase in PRS and corresponding liability r2 values of approximately 1%, suggesting at least a small polygenic contribution to DS-associated AVSD. Future studies with larger sample sizes will improve identification and quantification of genetic contributions to AVSD in DS.
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Affiliation(s)
- Cristina E Trevino
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Aaron M Holleman
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Holly Corbitt
- Division of Cardiovascular Medicine and the Heart Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Cheryl L Maslen
- Division of Cardiovascular Medicine and the Heart Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Tracie C Rosser
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Benjamin L Rambo-Martin
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Jai Oberoi
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Kenneth J Dooley
- Sibley Heart Center Cardiology, Department of Pediatrics, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | | | - Roger H Reeves
- Department of Physiology and the Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - A J Agopian
- Human Genetics Center; Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, TX, USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter J Gruber
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - James E O'Brien
- The Ward Family Heart Center, Section of Cardiac Surgery, Children's Mercy Hospital, Kansas City, MO, USA
| | - Douglas C Bittel
- College of Biosciences, Kansas City University of Medicine and Biosciences, Kansas City, MO, USA
| | | | - Clifford L Cua
- Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
| | - Stephanie L Sherman
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 300 Whitehead Biomedical Research Building, 615 Michael St., Atlanta, GA, 30322, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
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24
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Nees SN, Chung WK. Genetic Basis of Human Congenital Heart Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036749. [PMID: 31818857 DOI: 10.1101/cshperspect.a036749] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Congenital heart disease (CHD) is the most common major congenital anomaly with an incidence of ∼1% of live births and is a significant cause of birth defect-related mortality. The genetic mechanisms underlying the development of CHD are complex and remain incompletely understood. Known genetic causes include all classes of genetic variation including chromosomal aneuploidies, copy number variants, and rare and common single-nucleotide variants, which can be either de novo or inherited. Among patients with CHD, ∼8%-12% have a chromosomal abnormality or aneuploidy, between 3% and 25% have a copy number variation, and 3%-5% have a single-gene defect in an established CHD gene with higher likelihood of identifying a genetic cause in patients with nonisolated CHD. These genetic variants disrupt or alter genes that play an important role in normal cardiac development and in some cases have pleiotropic effects on other organs. This work reviews some of the most common genetic causes of CHD as well as what is currently known about the underlying mechanisms.
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Affiliation(s)
| | - Wendy K Chung
- Department of Pediatrics.,Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
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25
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Villar D, Frost S, Deloukas P, Tinker A. The contribution of non-coding regulatory elements to cardiovascular disease. Open Biol 2020; 10:200088. [PMID: 32603637 PMCID: PMC7574544 DOI: 10.1098/rsob.200088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Cardiovascular disease collectively accounts for a quarter of deaths worldwide. Genome-wide association studies across a range of cardiovascular traits and pathologies have highlighted the prevalence of common non-coding genetic variants within candidate loci. Here, we review genetic, epigenomic and molecular approaches to investigate the contribution of non-coding regulatory elements in cardiovascular biology. We then discuss recent insights on the emerging role of non-coding variation in predisposition to cardiovascular disease, with a focus on novel mechanistic examples from functional genomics studies. Lastly, we consider the clinical significance of these findings at present, and some of the current challenges facing the field.
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Affiliation(s)
- Diego Villar
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Stephanie Frost
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Panos Deloukas
- William Harvey Research Institute, Heart Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Andrew Tinker
- William Harvey Research Institute, Heart Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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26
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Agopian AJ, Hoang TT, Goldmuntz E, Hakonarson H, Musfee FI, Mitchell LE. X-chromosome association studies of congenital heart defects. Am J Med Genet A 2020; 182:250-254. [PMID: 31729158 PMCID: PMC7539172 DOI: 10.1002/ajmg.a.61411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 11/08/2022]
Affiliation(s)
- A. J. Agopian
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, Texas
| | - Thanh T. Hoang
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, Texas
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fadi I. Musfee
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, Texas
| | - Laura E. Mitchell
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, Texas
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27
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Nees SN, Chung WK. The genetics of isolated congenital heart disease. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 184:97-106. [PMID: 31876989 DOI: 10.1002/ajmg.c.31763] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [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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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: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [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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Lupo PJ, Mitchell LE, Jenkins MM. Genome-wide association studies of structural birth defects: A review and commentary. Birth Defects Res 2019; 111:1329-1342. [PMID: 31654503 DOI: 10.1002/bdr2.1606] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/21/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND While there is strong evidence that genetic risk factors play an important role in the etiologies of structural birth defects, compared to other diseases, there have been relatively few genome-wide association studies (GWAS) of these conditions. We reviewed the current landscape of GWAS conducted for birth defects, noting novel insights, and future directions. METHODS This article reviews the literature with regard to GWAS of structural birth defects. Key defects included in this review include oral clefts, congenital heart defects (CHDs), biliary atresia, pyloric stenosis, hypospadias, craniosynostosis, and clubfoot. Additionally, other issues related to GWAS are considered, including the assessment of polygenic risk scores and issues related to genetic ancestry, as well as utilizing genome-wide single nucleotide polymorphism array data to evaluate gene-environment interactions and Mendelian randomization. RESULTS For some birth defects, including oral clefts and CHDs, several novel susceptibility loci have been identified and replicated through GWAS, including 8q24 for oral clefts, DGKK for hypospadias, and 4p16 for CHDs. Relatively common birth defects for which there are currently no published GWAS include neural tube defects, anotia/microtia, anophthalmia/microphthalmia, gastroschisis, and omphalocele. CONCLUSIONS Overall, GWAS have been successful in identifying several novel susceptibility genes and genomic regions for structural birth defects. These findings have provided new insights into the etiologies of these phenotypes. However, GWAS have been underutilized for understanding the genetic etiologies of several birth defects.
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Affiliation(s)
- Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Laura E Mitchell
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia
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30
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Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects. PLoS One 2019; 14:e0219926. [PMID: 31314787 PMCID: PMC6636758 DOI: 10.1371/journal.pone.0219926] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/02/2019] [Indexed: 12/28/2022] Open
Abstract
Conotruncal heart defects (CTDs) are among the most common and severe groups of congenital heart defects. Despite evidence of an inherited genetic contribution to CTDs, little is known about the specific genes that contribute to the development of CTDs. We performed gene-based genome-wide analyses using microarray-genotyped and imputed common and rare variants data from two large studies of CTDs in the United States. We performed two case-parent trio analyses (N = 640 and 317 trios), using an extension of the family-based multi-marker association test, and two case-control analyses (N = 482 and 406 patients and comparable numbers of controls), using a sequence kernel association test. We also undertook two meta-analyses to combine the results from the analyses that used the same approach (i.e. family-based or case-control). To our knowledge, these analyses are the first reported gene-based, genome-wide association studies of CTDs. Based on our findings, we propose eight CTD candidate genes (ARF5, EIF4E, KPNA1, MAP4K3, MBNL1, NCAPG, NDFUS1 and PSMG3). Four of these genes (ARF5, KPNA1, NDUFS1 and PSMG3) have not been previously associated with normal or abnormal heart development. In addition, our analyses provide additional evidence that genes involved in chromatin-modification and in ribonucleic acid splicing are associated with congenital heart defects.
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31
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Chahal G, Tyagi S, Ramialison M. Navigating the non-coding genome in heart development and Congenital Heart Disease. Differentiation 2019; 107:11-23. [PMID: 31102825 DOI: 10.1016/j.diff.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Congenital Heart Disease (CHD) is characterised by a wide range of cardiac defects, from mild to life-threatening, which occur in babies worldwide. To date, there is no cure to CHD, however, progress in surgery has reduced its mortality allowing children affected by CHD to reach adulthood. In an effort to understand its genetic basis, several studies involving whole-genome sequencing (WGS) of patients with CHD have been undertaken and generated a great wealth of information. The majority of putative causative mutations identified in WGS studies fall into the non-coding part of the genome. Unfortunately, due to the lack of understanding of the function of these non-coding mutations, it is challenging to establish a causal link between the non-coding mutation and the disease. Thus, here we review the state-of-the-art approaches to interpret non-coding mutations in the context of CHD and address the following questions: What are the non-coding sequences important for cardiac function? Which technologies are used to identify them? Which resources are available to analyse them? What mutations are expected in these non-coding sequences? Learning from developmental process, what is their expected role in CHD?
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Affiliation(s)
- Gulrez Chahal
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Australian Genome Research Facility, 305 Grattan Street, Melbourne, VIC, 3000, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia.
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32
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Finney AC, Orr AW. Guidance Molecules in Vascular Smooth Muscle. Front Physiol 2018; 9:1311. [PMID: 30283356 PMCID: PMC6157320 DOI: 10.3389/fphys.2018.01311] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/30/2018] [Indexed: 12/21/2022] Open
Abstract
Several highly conserved families of guidance molecules, including ephrins, Semaphorins, Netrins, and Slits, play conserved and distinct roles in tissue remodeling during tissue patterning and disease pathogenesis. Primarily, these guidance molecules function as either secreted or surface-bound ligands that interact with their receptors to activate a variety of downstream effects, including cell contractility, migration, adhesion, proliferation, and inflammation. Vascular smooth muscle cells, contractile cells comprising the medial layer of the vessel wall and deriving from the mural population, regulate vascular tone and blood pressure. While capillaries lack a medial layer of vascular smooth muscle, mural-derived pericytes contribute similarly to capillary tone to regulate blood flow in various tissues. Furthermore, pericyte coverage is critical in vascular development, as perturbations disrupt vascular permeability and viability. During cardiovascular disease, smooth muscle cells play a more dynamic role in which suppression of contractile markers, enhanced proliferation, and migration lead to the progression of aberrant vascular remodeling. Since many types of guidance molecules are expressed in vascular smooth muscle and pericytes, these may contribute to blood vessel formation and aberrant remodeling during vascular disease. While vascular development is a large focus of the existing literature, studies emerged to address post-developmental roles for guidance molecules in pathology and are of interest as novel therapeutic targets. In this review, we will discuss the roles of guidance molecules in vascular smooth muscle and pericyte function in development and disease.
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Affiliation(s)
- Alexandra Christine Finney
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA, United States
| | - Anthony Wayne Orr
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA, United States
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA, United States
- Department of Pathology and Translational Medicine, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA, United States
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33
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Choy MK, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P, Keavney BD. Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks. Nat Commun 2018; 9:2526. [PMID: 29955040 PMCID: PMC6023870 DOI: 10.1038/s41467-018-04931-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 05/29/2018] [Indexed: 12/21/2022] Open
Abstract
Long-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression quantitative trait loci (eQTLs) in cardiac left ventricular tissue; captures the dynamic process of genome reorganisation after hESC-CM differentiation; overlaps genome-wide association study (GWAS) regions associated with heart rate; and identifies new candidate genes in such regions. These findings indicate that regulatory elements in hESC-CMs identified by our approach control gene expression involved in ventricular conduction and rhythm of the heart. The study of promoter interactions in other hESC-derived cell types may be of utility in functional investigation of GWAS-associated regions.
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Affiliation(s)
- Mun-Kit Choy
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK.
| | - Biola M Javierre
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Josep Carreras Leukaemia Research Institute, Campus ICO-Germans Trias I Pujol, Badalona, 08916, Barcelona, Spain
| | - Simon G Williams
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Stephanie L Baross
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Yingjuan Liu
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Chris Wallace
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Paula Freire-Pritchett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
- Department of Biological Science, Florida State University, Tallahassee, 32306, FL, USA.
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK.
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Fan SH, Shen ZY, Xiao YM. Functional polymorphisms of the neuropilin 1 gene are associated with the risk of tetralogy of Fallot in a Chinese Han population. Gene 2018; 653:72-79. [PMID: 29432830 DOI: 10.1016/j.gene.2018.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/22/2018] [Accepted: 02/08/2018] [Indexed: 01/07/2023]
Abstract
Tetralogy of Fallot (TOF) is one of the most severe forms of cyanotic congenital heart disease (CHD) and is also the most common. Previous genome-wide association study (GWAS) and replication studies have suggested that a polymorphism in the neuropilin 1 (NRP1) gene is significantly associated with the risk of TOF. To further confirm the association between the NRP1 polymorphism and the risk of TOF and to identify additional positive functional single-nucleotide polymorphisms (SNPs) for TOF risk, we systematically screened for functional polymorphisms throughout the regulatory and coding regions of the NRP1 gene. A total of 11 functional SNPs in 747 Chinese Han individuals, including 314 TOF patients and 433 healthy controls, were genotyped using the MassARRAY system and GeneScan. The results revealed that the allelic and genotypic frequencies of the NRP1 polymorphism rs2228638 were strongly associated with the risk of TOF (p = 0.002 and 0.001, respectively). To increase the robustness of rs2228638 as a TOF risk SNP, we conducted a meta-analysis that combined published studies and our current case-control study. The meta-analysis showed that the T allele of the NRP1 polymorphism rs2228638 was significantly associated with an increased risk of TOF in the combined population, which included European and Chinese Han individuals [combined p < 0.00001, odds ratio (OR) = 1.53, 95% confidence interval (95% CI) = 1.35-1.73]. In addition, the association analysis suggested for the first time that there is a strong association between the allele distribution of rs10080 and susceptibility to TOF (p = 0.001). Our data provide further evidence of the association between NRP1 polymorphisms and TOF risk, and suggest that rs2228638 may be an excellent marker for TOF risk in European and Chinese Han populations.
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Affiliation(s)
- Sai-Hou Fan
- Department of Adult Cardiac Surgery Center, Shanghai Yodak Cardiothoracic Hospital, Shanghai, PR China
| | - Zhen-Ya Shen
- Department of cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, Suzhou, Jiangsu, PR China.
| | - Yi-Min Xiao
- Department of Adult Cardiac Surgery Center, Shanghai Yodak Cardiothoracic Hospital, Shanghai, PR China
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Duran I, Tenney J, Warren CM, Sarukhanov A, Csukasi F, Skalansky M, Iruela-Arispe ML, Krakow D. NRP1 haploinsufficiency predisposes to the development of Tetralogy of Fallot. Am J Med Genet A 2018; 176:649-656. [PMID: 29363855 DOI: 10.1002/ajmg.a.38600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/16/2017] [Accepted: 12/12/2017] [Indexed: 01/13/2023]
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect. It involves anatomical abnormalities that change the normal flow of blood through the heart resulting in low oxygenation. Although not all of the underlying causes of TOF are completely understood, the disease has been associated with varying genetic etiologies including chromosomal abnormalities and Mendelian disorders, but can also occur as an isolated defect. In this report, we describe a familial case of TOF associated with a 1.8 Mb deletion of chromosome 10p11. Among the three genes in the region one is Neuropilin1 (NRP1), a membrane co-receptor of VEGF that modulates vasculogenesis. Hemizygous levels of NRP1 resulted in a reduced expression at the transcriptional and protein levels in patient-derived cells. Reduction of NRP1 also lead to decreased function of its activity as a co-receptor in intermolecular VEGF signaling. These findings support that diminished levels of NRP1 contribute to the development of TOF, likely through its function in mediating VEGF signal and vasculogenesis.
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Affiliation(s)
- Ivan Duran
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Jessica Tenney
- Department of Pediatrics, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Carmen M Warren
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California
| | - Anna Sarukhanov
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Fabiana Csukasi
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Mark Skalansky
- Department of Pediatrics, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Maria L Iruela-Arispe
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California
| | - Deborah Krakow
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California.,Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
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36
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Agopian AJ, Goldmuntz E, Hakonarson H, Sewda A, Taylor D, Mitchell LE. Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects. ACTA ACUST UNITED AC 2018; 10:e001449. [PMID: 28468790 DOI: 10.1161/circgenetics.116.001449] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 02/01/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Maternal and inherited (ie, case) genetic factors likely contribute to the pathogenesis of congenital heart defects, but it is unclear whether individual common variants confer a large risk. METHODS AND RESULTS To evaluate the relationship between individual common maternal/inherited genotypes and risk for heart defects, we conducted genome-wide association studies in 5 cohorts. Three cohorts were recruited at the Children's Hospital of Philadelphia: 670 conotruncal heart defect (CTD) case-parent trios, 317 left ventricular obstructive tract defect (LVOTD) case-parent trios, and 406 CTD cases (n=406) and 2976 pediatric controls. Two cohorts were recruited through the Pediatric Cardiac Genomics Consortium: 355 CTD trios and 192 LVOTD trios. We also conducted meta-analyses using the genome-wide association study results from the CTD cohorts, the LVOTD cohorts, and from the combined CTD and LVOTD cohorts. In the individual genome-wide association studies, several genome-wide significant associations (P≤5×10-8) were observed. In our meta-analyses, 1 genome-wide significant association was detected: the case genotype for rs72820264, an intragenetic single-nucleotide polymorphism associated with LVOTDs (P=2.1×10-8). CONCLUSIONS We identified 1 novel candidate region associated with LVOTDs and report on several additional regions with suggestive evidence for association with CTD and LVOTD. These studies were constrained by the relatively small samples sizes and thus have limited power to detect small to moderate associations. Approaches that minimize the multiple testing burden (eg, gene or pathway based) may, therefore, be required to uncover common variants contributing to the risk of these relatively rare conditions.
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Affiliation(s)
- A J Agopian
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Elizabeth Goldmuntz
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Hakon Hakonarson
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Anshuman Sewda
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Deanne Taylor
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA
| | - Laura E Mitchell
- From the Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston (A.J.A., A.S., L.E.M.); Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia (E.G.); and Division of Cardiology (E.G., H.H.), Center for Applied Genomics (H.H.), and Department of Biomedical and Health Informatics (D.T.), The Children's Hospital of Philadelphia, PA.
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Lebel M, Monnat RJ. Werner syndrome (WRN) gene variants and their association with altered function and age-associated diseases. Ageing Res Rev 2018; 41:82-97. [PMID: 29146545 DOI: 10.1016/j.arr.2017.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 01/14/2023]
Abstract
Werner syndrome (WS) is a heritable autosomal recessive human disorder characterized by the premature onset of several age-associated pathologies including cancer. The protein defective in WS patients, WRN, is encoded by a member of the human RECQ gene family that contains both a DNA exonuclease and a helicase domain. WRN has been shown to participate in several DNA metabolic pathways including DNA replication, recombination and repair, as well as telomere maintenance and transcription modulation. Here we review base pair-level genetic variation that has been documented in WRN, with an emphasis on non-synonymous coding single nucleotide polymorphisms (SNPs) and their associations with anthropomorphic features, longevity and disease risk. These associations have been challenging to identify, as many reported WRN SNP associations appear to be further conditioned upon ethnic, age, gender or other environmental co-variables. The WRN variant phenotypic associations identified to date are intriguing, and several are of clear clinical import. Consequently, it will be important to extend these initial associations and to identify the mechanisms and conditions under which specific WRN variants may compromise WRN function to drive cellular and organismal phenotypes as well as disease risk.
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Affiliation(s)
- Michel Lebel
- Centre de recherche du CHU de Québec, Pavillon CHUL Université Laval, Faculté de Médecine, Québec City, Québec, G1V 4G2, Canada.
| | - Raymond J Monnat
- Departments of Pathology and Genome Sciences, University of Washington, Seattle, WA 98195, USA
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McBride KL, Ware SM. Modifying Mendel Redux: Unbiased Approaches Can Find Modifiers. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.117.001891. [PMID: 29025762 DOI: 10.1161/circgenetics.117.001891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kim L McBride
- From the Center for Cardiovascular Research (K.L.M.) and Department of Pediatrics, College of Medicine (K.L.M.), Nationwide Children's Hospital, Ohio State University, Columbus; and Departments of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.).
| | - Stephanie M Ware
- From the Center for Cardiovascular Research (K.L.M.) and Department of Pediatrics, College of Medicine (K.L.M.), Nationwide Children's Hospital, Ohio State University, Columbus; and Departments of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
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Blue GM, Kirk EP, Giannoulatou E, Sholler GF, Dunwoodie SL, Harvey RP, Winlaw DS. Advances in the Genetics of Congenital Heart Disease: A Clinician's Guide. J Am Coll Cardiol 2017; 69:859-870. [PMID: 28209227 DOI: 10.1016/j.jacc.2016.11.060] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/18/2022]
Abstract
Our understanding of the genetics of congenital heart disease (CHD) is rapidly expanding; however, many questions, particularly those relating to sporadic forms of disease, remain unanswered. Massively parallel sequencing technology has made significant contributions to the field, both from a diagnostic perspective for patients and, importantly, also from the perspective of disease mechanism. The importance of de novo variation in sporadic disease is a recent highlight, and the genetic link between heart and brain development has been established. Furthermore, evidence of an underlying burden of genetic variation contributing to sporadic and familial forms of CHD has been identified. Although we are still unable to identify the cause of CHD for most patients, recent findings have provided us with a much clearer understanding of the types of variants and their individual contributions and collectively mark an important milestone in our understanding of both familial and sporadic forms of disease.
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Affiliation(s)
- Gillian M Blue
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - Edwin P Kirk
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney
| | - Gary F Sholler
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney
| | - David S Winlaw
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia.
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40
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Yang B, Zhou W, Jiao J, Nielsen JB, Mathis MR, Heydarpour M, Lettre G, Folkersen L, Prakash S, Schurmann C, Fritsche L, Farnum GA, Lin M, Othman M, Hornsby W, Driscoll A, Levasseur A, Thomas M, Farhat L, Dubé MP, Isselbacher EM, Franco-Cereceda A, Guo DC, Bottinger EP, Deeb GM, Booher A, Kheterpal S, Chen YE, Kang HM, Kitzman J, Cordell HJ, Keavney BD, Goodship JA, Ganesh SK, Abecasis G, Eagle KA, Boyle AP, Loos RJF, Eriksson P, Tardif JC, Brummett CM, Milewicz DM, Body SC, Willer CJ. Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve. Nat Commun 2017; 8:15481. [PMID: 28541271 PMCID: PMC5458508 DOI: 10.1038/ncomms15481] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/31/2017] [Indexed: 01/09/2023] Open
Abstract
Bicuspid aortic valve (BAV) is a heritable congenital heart defect and an important risk factor for valvulopathy and aortopathy. Here we report a genome-wide association scan of 466 BAV cases and 4,660 age, sex and ethnicity-matched controls with replication in up to 1,326 cases and 8,103 controls. We identify association with a noncoding variant 151 kb from the gene encoding the cardiac-specific transcription factor, GATA4, and near-significance for p.Ser377Gly in GATA4. GATA4 was interrupted by CRISPR-Cas9 in induced pluripotent stem cells from healthy donors. The disruption of GATA4 significantly impaired the transition from endothelial cells into mesenchymal cells, a critical step in heart valve development.
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Affiliation(s)
- Bo Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jiao Jiao
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jonas B. Nielsen
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Michael R. Mathis
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mahyar Heydarpour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada HIT 1C8
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada QC H3T 1J4
| | - Lasse Folkersen
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm SE-171 76, Sweden
- Center for Biological Sequence Analysis, Technical University of Denmark, Copenhagen DK-2800, Denmark
| | - Siddharth Prakash
- Department of Internal Medicine, Division of Medical Genetics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Lars Fritsche
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Gregory A. Farnum
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Maoxuan Lin
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan 48105, USA
| | - Whitney Hornsby
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Anisa Driscoll
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alexandra Levasseur
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Marc Thomas
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Linda Farhat
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, Quebec, Canada HIT 1C8
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada QC H3T 1J4
| | - Eric M. Isselbacher
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anders Franco-Cereceda
- Cardiothoracic Surgery Unit, Department of Molecular Medicine and Surgery, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Dong-chuan Guo
- Department of Internal Medicine, Division of Medical Genetics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - G. Michael Deeb
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Anna Booher
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sachin Kheterpal
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Y. Eugene Chen
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jacob Kitzman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne NE1 3BZ, UK
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Heart Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Judith A. Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne NE1 3BZ, UK
| | - Santhi K. Ganesh
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Gonçalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kim A. Eagle
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alan P. Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- The Mindich Child Health Development Institute, The Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Per Eriksson
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm SE-171 76, Sweden
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, Canada HIT 1C8
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada QC H3T 1J4
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dianna M. Milewicz
- Department of Internal Medicine, Division of Medical Genetics, University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA
| | - Simon C. Body
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cristen J. Willer
- Frankel Cardiovascular Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Blue GM, Humphreys D, Szot J, Major J, Chapman G, Bosman A, Kirk EP, Sholler GF, Harvey RP, Dunwoodie SL, Winlaw DS. The promises and challenges of exome sequencing in familial, non-syndromic congenital heart disease. Int J Cardiol 2016; 230:155-163. [PMID: 27989580 DOI: 10.1016/j.ijcard.2016.12.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/30/2016] [Accepted: 12/11/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Exome sequencing is an established strategy to identify causal variants in families with two or more members affected by congenital heart disease (CHD). This unbiased approach, in which both rare and common variants are identified, makes it suitable to research complex, heterogeneous diseases such as CHD. METHODS AND RESULTS Exome sequencing was performed on two affected members of a three generation family with atrial septal defects (ASD), suggesting a dominant inheritance pattern. Variants were filtered using two bioinformatics pipelines and prioritised according to in silico prediction programs. Segregation studies and functional analyses were used to assess co-segregation with disease and effects on protein function, respectively. Following the data and in silico analyses, ten candidate variants were prioritised. Of these, SRPK2 (c.2044C>T[p.Arg682Trp]) and NOTCH1 (c.3835C>T[p.Arg1279Cys]), co-segregated with disease in the family; however, previous functional analyses on SRPK2 make this an unlikely candidate. Functional analyses in the variant (c.3835C>T[p.Arg1279Cys]) of the known CHD gene NOTCH1 demonstrated a non-significant decrease in signalling activity. CONCLUSION This study demonstrates both the potential, as well as the challenges, of applying exome sequencing to complex diseases such as CHD. While in silico evidence and segregation analyses in the NOTCH1 p.Arg1279Cys variant are highly suggestive of pathogenicity, the minimal change in signalling capacity suggests that other variants may be required for CHD development. This study highlights the difficulties of applying exome sequencing in familial, non-syndromic CHD in the clinical environment and a cautionary note in the interpretation of apparently causal abnormalities in silico without supportive functional data.
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Affiliation(s)
- Gillian M Blue
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - David Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Justin Szot
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Joelene Major
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Alexis Bosman
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Edwin P Kirk
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Gary F Sholler
- The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - David S Winlaw
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia.
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Hanchard NA, Swaminathan S, Bucasas K, Furthner D, Fernbach S, Azamian MS, Wang X, Lewin M, Towbin JA, D'Alessandro LCA, Morris SA, Dreyer W, Denfield S, Ayres NA, Franklin WJ, Justino H, Lantin-Hermoso MR, Ocampo EC, Santos AB, Parekh D, Moodie D, Jeewa A, Lawrence E, Allen HD, Penny DJ, Fraser CD, Lupski JR, Popoola M, Wadhwa L, Brook JD, Bu'Lock FA, Bhattacharya S, Lalani SR, Zender GA, Fitzgerald-Butt SM, Bowman J, Corsmeier D, White P, Lecerf K, Zapata G, Hernandez P, Goodship JA, Garg V, Keavney BD, Leal SM, Cordell HJ, Belmont JW, McBride KL. A genome-wide association study of congenital cardiovascular left-sided lesions shows association with a locus on chromosome 20. Hum Mol Genet 2016; 25:2331-2341. [PMID: 26965164 DOI: 10.1093/hmg/ddw071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 02/26/2016] [Indexed: 12/28/2022] Open
Abstract
Congenital heart defects involving left-sided lesions (LSLs) are relatively common birth defects with substantial morbidity and mortality. Previous studies have suggested a high heritability with a complex genetic architecture, such that only a few LSL loci have been identified. We performed a genome-wide case-control association study to address the role of common variants using a discovery cohort of 778 cases and 2756 controls. We identified a genome-wide significant association mapping to a 200 kb region on chromosome 20q11 [P= 1.72 × 10-8 for rs3746446; imputed Single Nucleotide Polymorphism (SNP) rs6088703 P= 3.01 × 10-9, odds ratio (OR)= 1.6 for both]. This result was supported by transmission disequilibrium analyses using a subset of 541 case families (lowest P in region= 4.51 × 10-5, OR= 1.5). Replication in a cohort of 367 LSL cases and 5159 controls showed nominal association (P= 0.03 for rs3746446) resulting in P= 9.49 × 10-9 for rs3746446 upon meta-analysis of the combined cohorts. In addition, a group of seven SNPs on chromosome 1q21.3 met threshold for suggestive association (lowest P= 9.35 × 10-7 for rs12045807). Both regions include genes involved in cardiac development-MYH7B/miR499A on chromosome 20 and CTSK, CTSS and ARNT on chromosome 1. Genome-wide heritability analysis using case-control genotyped SNPs suggested that the mean heritability of LSLs attributable to common variants is moderately high ([Formula: see text] range= 0.26-0.34) and consistent with previous assertions. These results provide evidence for the role of common variation in LSLs, proffer new genes as potential biological candidates, and give further insight to the complex genetic architecture of congenital heart disease.
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Affiliation(s)
- Neil A Hanchard
- Department of Molecular and Human Genetics, Department of Pediatrics
| | | | - Kristine Bucasas
- Department of Molecular and Human Genetics, Center for Statistical Genetics
| | - Dieter Furthner
- Department of Paediatrics, Children's Hospital, Linz, Austria
| | | | | | | | - Mark Lewin
- Division of Cardiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Jeffrey A Towbin
- Pediatric Cardiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | | | | | | | - Nancy A Ayres
- Division of Cardiology, Department of Pediatrics, and
| | | | - Henri Justino
- Division of Cardiology, Department of Pediatrics, and
| | | | | | | | - Dhaval Parekh
- Division of Cardiology, Department of Pediatrics, and
| | | | - Aamir Jeewa
- Division of Cardiology, Department of Pediatrics, and
| | | | - Hugh D Allen
- Division of Cardiology, Department of Pediatrics, and
| | | | - Charles D Fraser
- Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Department of Pediatrics
| | | | - Lalita Wadhwa
- Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - J David Brook
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Frances A Bu'Lock
- East Midlands Congenital Heart Centre, Glenfield Hospital, Leicester, UK
| | - Shoumo Bhattacharya
- Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Sara M Fitzgerald-Butt
- Department of Pediatrics and Center for Cardiovascular and Pulmonary Research, The Heart Center, and
| | | | - Don Corsmeier
- Department of Pediatrics and Center for Microbial Pathogenesis, Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter White
- Department of Pediatrics and Center for Microbial Pathogenesis, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kelsey Lecerf
- College of Medicine, Ohio State University, Columbus, OH, USA
| | - Gladys Zapata
- Department of Molecular and Human Genetics, Department of Pediatrics
| | | | - Judith A Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK and
| | - Vidu Garg
- Department of Pediatrics and Center for Cardiovascular and Pulmonary Research, The Heart Center, and
| | - Bernard D Keavney
- Institute of Cardiovascular Sciences, The University of Manchester, Manchester, UK
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Center for Statistical Genetics
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK and
| | - John W Belmont
- Department of Molecular and Human Genetics, Department of Pediatrics,
| | - Kim L McBride
- Department of Pediatrics and Center for Cardiovascular and Pulmonary Research,
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Mlynarski EE, Xie M, Taylor D, Sheridan MB, Guo T, Racedo SE, McDonald-McGinn DM, Chow EWC, Vorstman J, Swillen A, Devriendt K, Breckpot J, Digilio MC, Marino B, Dallapiccola B, Philip N, Simon TJ, Roberts AE, Piotrowicz M, Bearden CE, Eliez S, Gothelf D, Coleman K, Kates WR, Devoto M, Zackai E, Heine-Suñer D, Goldmuntz E, Bassett AS, Morrow BE, Emanuel BS. Rare copy number variants and congenital heart defects in the 22q11.2 deletion syndrome. Hum Genet 2016; 135:273-85. [PMID: 26742502 DOI: 10.1007/s00439-015-1623-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022]
Abstract
The 22q11.2 deletion syndrome (22q11DS; velocardiofacial/DiGeorge syndrome; VCFS/DGS; MIM #192430; 188400) is the most common microdeletion syndrome. The phenotypic presentation of 22q11DS is highly variable; approximately 60-75 % of 22q11DS patients have been reported to have a congenital heart defect (CHD), mostly of the conotruncal type, and/or aortic arch defect. The etiology of the cardiac phenotypic variability is not currently known for the majority of patients. We hypothesized that rare copy number variants (CNVs) outside the 22q11.2 deleted region may modify the risk of being born with a CHD in this sensitized population. Rare CNV analysis was performed using Affymetrix SNP Array 6.0 data from 946 22q11DS subjects with CHDs (n = 607) or with normal cardiac anatomy (n = 339). Although there was no significant difference in the overall burden of rare CNVs, an overabundance of CNVs affecting cardiac-related genes was detected in 22q11DS individuals with CHDs. When the rare CNVs were examined with regard to gene interactions, specific cardiac networks, such as Wnt signaling, appear to be overrepresented in 22q11DS CHD cases but not 22q11DS controls with a normal heart. Collectively, these data suggest that CNVs outside the 22q11.2 region may contain genes that modify risk for CHDs in some 22q11DS patients.
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Affiliation(s)
- Elisabeth E Mlynarski
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Molly B Sheridan
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Silvia E Racedo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eva W C Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Jacob Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584, Utrecht, The Netherlands
| | - Ann Swillen
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | | | - Bruno Marino
- Lorillard Spencer Cenci Foundation and Department of Pediatrics, La Sapienza University of Rome, 00165, Rome, Italy
| | | | - Nicole Philip
- Department of Medical Genetics, Timone Children's Hospital, AP-HM and University of Mediterranee, 13005, Marseille, France
| | - Tony J Simon
- Department of Psychiatry and Behavioral Sciences, M.I.N.D. Institute, University of California, Sacramento, CA, 95817, USA
| | - Amy E Roberts
- Department of Cardiology and Division of Genetics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Małgorzata Piotrowicz
- Department of Genetics, Research Institute, Polish Mother's Memorial Hospital, 93-338, Lodz, Poland
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA
| | - Stephan Eliez
- Office Médico- Pédagogique Research Unit, Department of Psychiatry, University of Geneva School of Medicine, 1211, Geneva 8, Switzerland
| | - Doron Gothelf
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, 52621, Tel Aviv, Israel
| | - Karlene Coleman
- Marcus Autism Center, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, and Program in Neuroscience, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Molecular Medicine, University of Rome La Sapienza, 00185, Rome, Italy
| | - Elaine Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Damian Heine-Suñer
- Genetics Department, Hospital Universitari Son Espases, 07020, Palma de Mallorca, Spain
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Howey R, Mamasoula C, Töpf A, Nudel R, Goodship J, Keavney B, Cordell H. Increased Power for Detection of Parent-of-Origin Effects via the Use of Haplotype Estimation. Am J Hum Genet 2015; 97:419-34. [PMID: 26320892 PMCID: PMC4564992 DOI: 10.1016/j.ajhg.2015.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/29/2015] [Indexed: 01/02/2023] Open
Abstract
Parent-of-origin (or imprinting) effects relate to the situation in which traits are influenced by the allele inherited from only one parent and the allele from the other parent has little or no effect. Given SNP genotype data from case-parent trios, the parent of origin of each allele in the offspring can often be deduced unambiguously; however, this is not true when all three individuals are heterozygous. Most existing methods for investigating parent-of-origin effects operate on a SNP-by-SNP basis and either perform some sort of averaging over the possible parental transmissions or else discard ambiguous trios. If the correct parent of origin at a SNP could be determined, this would provide extra information and increase the power for detecting the effects of imprinting. We propose making use of the surrounding SNP information, via haplotype estimation, to improve estimation of parent of origin at a test SNP for case-parent trios, case-mother duos, and case-father duos. This extra information is then used in a multinomial modeling approach for estimating parent-of-origin effects at the test SNP. We show through computer simulations that our approach has increased power over previous approaches, particularly when the data consist only of duos. We apply our method to two real datasets and find a decrease in significance of p values in genomic regions previously thought to possibly harbor imprinting effects, thus weakening the evidence that such effects actually exist in these regions, although some regions retain evidence of significant effects.
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Strate I, Tessadori F, Bakkers J. Glypican4 promotes cardiac specification and differentiation by attenuating canonical Wnt and Bmp signaling. Development 2015; 142:1767-76. [PMID: 25968312 DOI: 10.1242/dev.113894] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glypicans are heparan sulphate proteoglycans (HSPGs) attached to the cell membrane by a glycosylphosphatidylinositol (GPI) anchor, and interact with various extracellular growth factors and receptors. The Drosophila division abnormal delayed (dally) was the first glypican loss-of-function mutant described that displays disrupted cell divisions in the eye and morphological defects in the wing. In human, as in most vertebrates, six glypican-encoding genes have been identified (GPC1-6), and mutations in several glypican genes cause multiple malformations including congenital heart defects. To understand better the role of glypicans during heart development, we studied the zebrafish knypek mutant, which is deficient for Gpc4. Our results demonstrate that knypek/gpc4 mutant embryos display severe cardiac defects, most apparent by a strong reduction in cardiomyocyte numbers. Cell-tracing experiments, using photoconvertable fluorescent proteins and genetic labeling, demonstrate that Gpc4 'Knypek' is required for specification of cardiac progenitor cells and their differentiation into cardiomyocytes. Mechanistically, we show that Bmp signaling is enhanced in the anterior lateral plate mesoderm of knypek/gpc4 mutants and that genetic inhibition of Bmp signaling rescues the cardiomyocyte differentiation defect observed in knypek/gpc4 embryos. In addition, canonical Wnt signaling is upregulated in knypek/gpc4 embryos, and inhibiting canonical Wnt signaling in knypek/gpc4 embryos by overexpression of the Wnt inhibitor Dkk1 restores normal cardiomyocyte numbers. Therefore, we conclude that Gpc4 is required to attenuate both canonical Wnt and Bmp signaling in the anterior lateral plate mesoderm to allow cardiac progenitor cells to specify and differentiate into cardiomyocytes. This provides a possible explanation for how congenital heart defects arise in glypican-deficient patients.
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Affiliation(s)
- Ina Strate
- Department of Cardiac Development and Genetics, Hubrecht Institute & University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Federico Tessadori
- Department of Cardiac Development and Genetics, Hubrecht Institute & University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Jeroen Bakkers
- Department of Cardiac Development and Genetics, Hubrecht Institute & University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands Department of Medical Physiology, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands
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46
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Association analysis identifies new risk loci for congenital heart disease in Chinese populations. Nat Commun 2015; 6:8082. [PMID: 26283027 DOI: 10.1038/ncomms9082] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 07/15/2015] [Indexed: 01/08/2023] Open
Abstract
Our previous genome-wide association study (GWAS) identified two susceptibility loci for congenital heart disease (CHD) in Han Chinese. Here we identify additional loci by testing promising associations in an extended 3-stage validation consisting of 6,053 CHD cases and 7,410 controls. We find GW significant (P<5.0 × 10(-8)) evidence of 4 additional CHD susceptibility loci at 4q31.22 (rs1400558, upstream of EDNRA, Pall=1.63 × 10(-9)), 9p24.2 (rs7863990, close to SMARCA2, Pall=3.71 × 10(-14)), 12q24.13 (rs2433752, upstream of TBX3 and TBX5, Pall=1.04 × 10(-10)) and 20q12 (rs490514, in PTPRT, Pall=1.20 × 10(-13)). Moreover, the data from previous European GWAS supports that rs490514 is associated with the risk of CHD (P=3.40 × 10(-3)). These results enhance our understanding of CHD susceptibility.
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Abstract
Congenital heart disease (CHD) is the most common type of birth defect. The advent of corrective cardiac surgery and the increase in knowledge concerning the longitudinal care of patients with CHD has led to a spectacular increase in life expectancy. Therefore, >90% of children with CHD, who survive the first year of life, will live into adulthood. The etiology of CHD is complex and is associated with both environmental and genetic causes. CHD is a genetically heterogeneous disease that is associated with long-recognized chromosomal abnormalities, as well as with mutation in numerous (developmental) genes. Nevertheless, the genetic factors underlying CHD have remained largely elusive, and it is important to realize that in the far majority of CHD patients no causal mutation or chromosomal abnormality is identified. However, new insights (alternative inheritance paradigms) and technology (next-generation sequencing) have become available that can greatly advance our understanding of the genetic factors that contribute to CHD; these will be discussed in this review. Moreover, we will focus on the discovery of regulatory regions of key (heart) developmental genes and the occurrence of variations and mutations within, in the setting of CHD.
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Genome-Wide Association Study of Down Syndrome-Associated Atrioventricular Septal Defects. G3-GENES GENOMES GENETICS 2015; 5:1961-71. [PMID: 26194203 PMCID: PMC4592978 DOI: 10.1534/g3.115.019943] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The goal of this study was to identify the contribution of common genetic variants to Down syndrome−associated atrioventricular septal defect, a severe heart abnormality. Compared with the euploid population, infants with Down syndrome, or trisomy 21, have a 2000-fold increased risk of presenting with atrioventricular septal defects. The cause of this increased risk remains elusive. Here we present data from the largest heart study conducted to date on a trisomic background by using a carefully characterized collection of individuals from extreme ends of the phenotypic spectrum. We performed a genome-wide association study using logistic regression analysis on 452 individuals with Down syndrome, consisting of 210 cases with complete atrioventricular septal defects and 242 controls with structurally normal hearts. No individual variant achieved genome-wide significance. We identified four disomic regions (1p36.3, 5p15.31, 8q22.3, and 17q22) and two trisomic regions on chromosome 21 (around PDXK and KCNJ6 genes) that merit further investigation in large replication studies. Our data show that a few common genetic variants of large effect size (odds ratio >2.0) do not account for the elevated risk of Down syndrome−associated atrioventricular septal defects. Instead, multiple variants of low-to-moderate effect sizes may contribute to this elevated risk, highlighting the complex genetic architecture of atrioventricular septal defects even in the highly susceptible Down syndrome population.
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49
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Tetralogy of Fallot, microcephaly, short stature and brachymesophalangy is associated with hemizygous loss of noncoding MIR17HG and coding GPC5. Clin Dysmorphol 2015; 24:113-4. [DOI: 10.1097/mcd.0000000000000069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Lahm H, Schön P, Doppler S, Dreßen M, Cleuziou J, Deutsch MA, Ewert P, Lange R, Krane M. Tetralogy of Fallot and Hypoplastic Left Heart Syndrome - Complex Clinical Phenotypes Meet Complex Genetic Networks. Curr Genomics 2015; 16:141-58. [PMID: 26069455 PMCID: PMC4460219 DOI: 10.2174/1389202916666150303232520] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 01/06/2023] Open
Abstract
In many cases congenital heart disease (CHD) is represented by a complex phenotype and
an array of several functional and morphological cardiac disorders. These malformations will be
briefly summarized in the first part focusing on two severe CHD phenotypes, hypoplastic left heart
syndrome (HLHS) and tetralogy of Fallot (TOF). In most cases of CHD the genetic origin remains
largely unknown, though the complexity of the clinical picture strongly argues against a dysregulation which can be attributed
to a single candidate gene but rather suggests a multifaceted polygenetic origin with elaborate interactions. Consistent
with this idea, genome-wide approaches using whole exome sequencing, comparative sequence analysis of multiplex
families to identify de novo mutations and global technologies to identify single nucleotide polymorphisms, copy
number variants, dysregulation of the transcriptome and epigenetic variations have been conducted to obtain information
about genetic alterations and potential predispositions possibly linked to the occurrence of a CHD phenotype. In the second
part of this review we will summarize and discuss the available literature on identified genetic alterations linked to
TOF and HLHS.
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Affiliation(s)
- Harald Lahm
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Patric Schön
- Department of Paediatric Cardiology and Congenital Heart Defects, German Heart Center Munich, Technische Universität München, D-80636 Munich, Germany
| | - Stefanie Doppler
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Julie Cleuziou
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Marcus-André Deutsch
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Peter Ewert
- Department of Paediatric Cardiology and Congenital Heart Defects, German Heart Center Munich, Technische Universität München, D-80636 Munich, Germany; ; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart Alliance, Munich, Germany
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany; ; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart Alliance, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany; ; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart Alliance, Munich, Germany
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