1
|
Chen X, Li Y, Xu J, Cui Y, Wu Q, Yin H, Li Y, Gao C, Jiang L, Wang H, Wen Z, Yao Z, Wu Z. Styxl2 regulates de novo sarcomere assembly by binding to non-muscle myosin IIs and promoting their degradation. eLife 2024; 12:RP87434. [PMID: 38829202 PMCID: PMC11147509 DOI: 10.7554/elife.87434] [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] [Indexed: 06/05/2024] Open
Abstract
Styxl2, a poorly characterized pseudophosphatase, was identified as a transcriptional target of the Jak1-Stat1 pathway during myoblast differentiation in culture. Styxl2 is specifically expressed in vertebrate striated muscles. By gene knockdown in zebrafish or genetic knockout in mice, we found that Styxl2 plays an essential role in maintaining sarcomere integrity in developing muscles. To further reveal the functions of Styxl2 in adult muscles, we generated two inducible knockout mouse models: one with Styxl2 being deleted in mature myofibers to assess its role in sarcomere maintenance, and the other in adult muscle satellite cells (MuSCs) to assess its role in de novo sarcomere assembly. We find that Styxl2 is not required for sarcomere maintenance but functions in de novo sarcomere assembly during injury-induced muscle regeneration. Mechanistically, Styxl2 interacts with non-muscle myosin IIs, enhances their ubiquitination, and targets them for autophagy-dependent degradation. Without Styxl2, the degradation of non-muscle myosin IIs is delayed, which leads to defective sarcomere assembly and force generation. Thus, Styxl2 promotes de novo sarcomere assembly by interacting with non-muscle myosin IIs and facilitating their autophagic degradation.
Collapse
Affiliation(s)
- Xianwei Chen
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Yanfeng Li
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Jin Xu
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Yong Cui
- School of Life Sciences, Chinese University of Hong KongHong KongChina
| | - Qian Wu
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic UniversityHong KongChina
| | - Haidi Yin
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic UniversityHong KongChina
| | - Yuying Li
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong KongHong KongChina
| | - Chuan Gao
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Liwen Jiang
- School of Life Sciences, Chinese University of Hong KongHong KongChina
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong KongHong KongChina
| | - Zilong Wen
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| | - Zhongping Yao
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic UniversityHong KongChina
| | - Zhenguo Wu
- Division of Life Science, Hong Kong University of Science & TechnologyHong KongChina
| |
Collapse
|
2
|
Heshmatzad K, Naderi N, Maleki M, Abbasi S, Ghasemi S, Ashrafi N, Fazelifar AF, Mahdavi M, Kalayinia S. Role of non-coding variants in cardiovascular disease. J Cell Mol Med 2023; 27:1621-1636. [PMID: 37183561 PMCID: PMC10273088 DOI: 10.1111/jcmm.17762] [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: 10/31/2022] [Revised: 03/29/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
Cardiovascular diseases (CVDs) constitute one of the significant causes of death worldwide. Different pathological states are linked to CVDs, which despite interventions and treatments, still have poor prognoses. The genetic component, as a beneficial tool in the risk stratification of CVD development, plays a role in the pathogenesis of this group of diseases. The emergence of genome-wide association studies (GWAS) have led to the identification of non-coding parts associated with cardiovascular traits and disorders. Variants located in functional non-coding regions, including promoters/enhancers, introns, miRNAs and 5'/3' UTRs, account for 90% of all identified single-nucleotide polymorphisms associated with CVDs. Here, for the first time, we conducted a comprehensive review on the reported non-coding variants for different CVDs, including hypercholesterolemia, cardiomyopathies, congenital heart diseases, thoracic aortic aneurysms/dissections and coronary artery diseases. Additionally, we present the most commonly reported genes involved in each CVD. In total, 1469 non-coding variants constitute most reports on familial hypercholesterolemia, hypertrophic cardiomyopathy and dilated cardiomyopathy. The application and identification of non-coding variants are beneficial for the genetic diagnosis and better therapeutic management of CVDs.
Collapse
Affiliation(s)
- Katayoun Heshmatzad
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Niloofar Naderi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Majid Maleki
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Shiva Abbasi
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Serwa Ghasemi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Nooshin Ashrafi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Amir Farjam Fazelifar
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Mohammad Mahdavi
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| |
Collapse
|
3
|
Zuo JY, Chen HX, Liu ZG, Yang Q, He GW. Identification and functional analysis of variants of MYH6 gene promoter in isolated ventricular septal defects. BMC Med Genomics 2022; 15:213. [PMID: 36209093 PMCID: PMC9548206 DOI: 10.1186/s12920-022-01365-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/21/2022] [Indexed: 11/11/2022] Open
Abstract
Background Ventricular septal defect is the most common form of congenital heart diseases. MYH6 gene has a critical effect on the growth and development of the heart but the variants in the promoter of MYH6 is unknown. Patients and methods In 604 of the subjects (311 isolated and sporadic ventricular septal defect patients and 293 healthy controls), DNA was extracted from blood samples and MYH6 gene promoter region variants were analyzed by sequencing. Further functional verification was performed by cellular experiments using dual luciferase reporter gene analysis, electrophoretic mobility shift assays, and bioinformatics analysis. Results Nine variants were identified in the MYH6 gene promoter and two of those variants [g.4085G>C(rs1222539675) and g.4716G>A(rs377648095)] were only found in the ventricular septal defect patients. Cellular function experiments showed that these two variants reduced the transcriptional activity of the MYH6 gene promoter (p < 0.001). Further analysis with online JASPAR database suggests that these variants may alter a set of putative transcription factor binding sites that possibly lead to changes in myosin subunit expression and ventricular septal defect formation. Conclusions Our study for the first time identifies variants in the promoter region of the MYH6 gene in Chinese patients with isolated and sporadic ventricular septal defect. These variants significantly reduced MYH6 gene expression and affected transcription factor binding sites and therefore are pathogenic. The present study provides new insights in the role of the MYH6 gene promoter region to better understand the genetic basis of VSD formation. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01365-y.
Collapse
Affiliation(s)
- Ji-Yang Zuo
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China.,Clinical School of Cardiovascular Disease, Tianjin Medical University, Tianjin, China
| | - Huan-Xin Chen
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Zhi-Gang Liu
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Qin Yang
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Guo-Wei He
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China.
| |
Collapse
|
4
|
Banerjee S, Prabhu Basrur N, Rai PS. Omics technologies in personalized combination therapy for cardiovascular diseases: challenges and opportunities. Per Med 2021; 18:595-611. [PMID: 34689602 DOI: 10.2217/pme-2021-0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The primary purpose of 'omics' technologies is to understand the intricacy of genomics, proteomics, metabolomics and other molecular mechanisms to reveal the complex traits of human diseases. The significant use of omics technologies and their applications in medicine gear up the study of the pathogenesis of several disorders. The detection of biomarkers in the early onset of diseases is challenging; still, omics can discover novel molecular mechanisms and biomarkers. In this review, the different types of omics and their technologies are explicated and aimed to provide their emerging applications in cardiovascular precision medicine. These technologies significantly impact optimizing medical treatment for individuals to reach a higher level in precision medicine.
Collapse
Affiliation(s)
- Saradindu Banerjee
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Navya Prabhu Basrur
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| |
Collapse
|
5
|
Huang S, Wu Y, Chen S, Yang Y, Wang Y, Wang H, Li P, Zhuang J, Xia Y. Novel insertion mutation (Arg1822_Glu1823dup) in MYH6 coiled-coil domain causing familial atrial septal defect. Eur J Med Genet 2021; 64:104314. [PMID: 34481090 DOI: 10.1016/j.ejmg.2021.104314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Atrial septal defect, secundum (ASD Ⅱ, OMIM: 603642) is the second common congenital heart defect (CHD) in China. However, the genetic etiology of familial ASD II remains elusive. METHODS AND RESULTS Using whole-exome sequencing (WES) and Sanger sequencing, we identified a novel myosin heavy chain 6 (MYH6) gene insertion variation, NM_002471.3: c.5465_5470dup (Arg1822_Glu1823dup), in a large Chinese Han family with ASD II. The variant Arg1822_Glu1823dup co-segregated with the disease in this family with autosomal dominant inheritance. The insertion variant located in the coiled-coil domain of the MYH6 protein, which is highly conserved across homologous myosin proteins and species. In transfected myoblast C2C12 cell lines, the MYH6 Arg1822_Glu1823dup variant significantly impaired myofibril formation and increased apoptosis but did not significantly reduce cell viability. Furthermore, molecular simulations revealed that the Arg1822_Glu1823dup variant impaired the myosin α-helix, increasing the stability of the coiled-coil myosin dimer, suggesting that this variant has an effect on the coiled-coil domain self-aggregation. These findings indicate that Arg1822_Glu1823dup variant plays a crucial role in the pathogenesis of ASD II. CONCLUSION Our findings expand the spectrum of MYH6 variations associated with familial ASD II and may provide a molecular basis in genetic counseling and prenatal diagnosis for this Chinses family.
Collapse
Affiliation(s)
- Shufang Huang
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yueheng Wu
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shaoxian Chen
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yongchao Yang
- Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Disease Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yonghua Wang
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Haiping Wang
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ping Li
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Disease Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yu Xia
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China; The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| |
Collapse
|
6
|
The role of DNA methylation in syndromic and non-syndromic congenital heart disease. Clin Epigenetics 2021; 13:93. [PMID: 33902696 PMCID: PMC8077695 DOI: 10.1186/s13148-021-01077-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
Congenital heart disease (CHD) is a common structural birth defect worldwide, and defects typically occur in the walls and valves of the heart or enlarged blood vessels. Chromosomal abnormalities and genetic mutations only account for a small portion of the pathogenic mechanisms of CHD, and the etiology of most cases remains unknown. The role of epigenetics in various diseases, including CHD, has attracted increased attention. The contributions of DNA methylation, one of the most important epigenetic modifications, to CHD have not been illuminated. Increasing evidence suggests that aberrant DNA methylation is related to CHD. Here, we briefly introduce DNA methylation and CHD and then review the DNA methylation profiles during cardiac development and in CHD, abnormalities in maternal genome-wide DNA methylation patterns are also described. Whole genome methylation profile and important differentially methylated genes identified in recent years are summarized and clustered according to the sample type and methodologies. Finally, we discuss the novel technology for and prospects of CHD-related DNA methylation.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Application of next-generation sequencing for the diagnosis of fetuses with congenital heart defects. Curr Opin Obstet Gynecol 2020; 31:132-138. [PMID: 30608255 DOI: 10.1097/gco.0000000000000520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Congenital heart defects (CHDs) are the most common type of birth defects, and are thought to result from genetic-environmental interactions. Currently, karyotype and chromosomal microarray analyses are the primary methods used to detect chromosomal abnormalities and copy number variations in fetuses with CHD. Recently, with the introduction of next-generation sequencing (NGS) in prenatal diagnosis, gene mutations have been identified in cases of CHD. The purpose of this review is to summarize current studies about the genetic cause of fetal CHD, paying particular attention to the application of NGS for fetuses with CHD. RECENT FINDINGS In addition to chromosomal abnormalities, gene mutations are an important genetic cause of fetal CHD. Furthermore, incidences of pathogenic mutations in fetuses with CHD are associated with the presence of other structural anomalies, but are irrelevant to the categories of CHD. SUMMARY Gene mutations are important causes of fetal CHD and NGS should be applied to all fetuses with normal karyotype and copy number variations, regardless of whether the CHD is isolated or syndromic.
Collapse
|
9
|
Kalayinia S, Maleki M, Mahdavi M, Mahdieh N. A novel de novo dominant mutation of NOTCH1 gene in an Iranian family with non-syndromic congenital heart disease. J Clin Lab Anal 2019; 34:e23147. [PMID: 31867804 PMCID: PMC7171333 DOI: 10.1002/jcla.23147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/10/2019] [Accepted: 11/16/2019] [Indexed: 12/16/2022] Open
Abstract
Background Congenital heart disease (CHD) is the most common birth defect which can arises from different genetic defects. The genetic heterogeneity of this disease leads to restricted success in candidate genes screening method. Emerging approaches such as next‐generation sequencing (NGS)‐based genetic analysis might provide a better understating of CHD etiology in the patients who are left undiagnosed. To this aim, in this study, we survived the causes of CHD in an Iranian family who was consanguineous and had two affected children. Methods Affected individuals of this family were checked previously by PCR‐direct sequencing for six candidate genes (NKX2‐5, ZIC3, NODAL, FOXH1, GJA1, GATA4) and had not revealed any reported CHD causative mutations. Whole‐exome sequencing (WES) was performed on this family probond to determine the underlying cause of CHD, and the identified variants were confirmed and segregated by Sanger sequencing. Results We identified one heterozygous missense mutation, c.T6797C (p.Phe2266Ser), in the NOTCH1 gene, which seems to be the most probably disease causing of this family patients. This mutation was found to be novel and not reported on 1000 Genomes Project, dbSNP, and ExAC. Conclusion Worldwide, mutations in NOTCH1 gene are considered as one of the most known causes of CHD. The found NOTCH1 variant in this family affected individuals was the first report from Iran. Yet again, this result indicates the importance of NOTCH1 screening in CHD patients.
Collapse
Affiliation(s)
- Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahdavi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Nejat Mahdieh
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
10
|
Bjornsson T, Thorolfsdottir RB, Sveinbjornsson G, Sulem P, Norddahl GL, Helgadottir A, Gretarsdottir S, Magnusdottir A, Danielsen R, Sigurdsson EL, Adalsteinsdottir B, Gunnarsson SI, Jonsdottir I, Arnar DO, Helgason H, Gudbjartsson T, Gudbjartsson DF, Thorsteinsdottir U, Holm H, Stefansson K. A rare missense mutation in MYH6 associates with non-syndromic coarctation of the aorta. Eur Heart J 2019; 39:3243-3249. [PMID: 29590334 PMCID: PMC6127890 DOI: 10.1093/eurheartj/ehy142] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
Aims Coarctation of the aorta (CoA) accounts for 4–8% of congenital heart defects (CHDs) and confers substantial morbidity despite treatment. It is increasingly recognized as a highly heritable condition. The aim of the study was to search for sequence variants that affect the risk of CoA. Methods and results We performed a genome-wide association study of CoA among Icelanders (120 cases and 355 166 controls) based on imputed variants identified through whole-genome sequencing. We found association with a rare (frequency = 0.34%) missense mutation p.Arg721Trp in MYH6 (odds ratio = 44.2, P = 5.0 × 10−22), encoding the alpha-heavy chain subunit of cardiac myosin, an essential sarcomere protein. Approximately 20% of individuals with CoA in Iceland carry this mutation. We show that p.Arg721Trp also associates with other CHDs, in particular bicuspid aortic valve. We have previously reported broad effects of p.Arg721Trp on cardiac electrical function and strong association with sick sinus syndrome and atrial fibrillation. Conclusion Through a population approach, we found that a rare missense mutation p.Arg721Trp in the sarcomere gene MYH6 has a strong effect on the risk of CoA and explains a substantial fraction of the Icelanders with CoA. This is the first mutation associated with non-familial or sporadic form of CoA at a population level. The p.Arg721Trp in MYH6 causes a cardiac syndrome with highly variable expressivity and emphasizes the importance of sarcomere integrity for cardiac development and function.
Collapse
Affiliation(s)
| | | | | | - Patrick Sulem
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland
| | | | | | | | | | - Ragnar Danielsen
- Department of Medicine, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Emil L Sigurdsson
- Department of Family Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland.,Department of Development, Primary Health Care of the Capital Area, Alfabakki 16, Reykjavik, Iceland
| | - Berglind Adalsteinsdottir
- Department of Cardiology, Haukeland University Hospital, Jonas Lies vei 83, Bergen, Norway.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
| | - Sverrir I Gunnarsson
- Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin, 600 Highland Ave, Madison, WI, USA
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland.,Department of Immunology, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - David O Arnar
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Department of Medicine, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
| | - Hrodmar Helgason
- Children's Hospital, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Tomas Gudbjartsson
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland.,Department of Cardiothoracic Surgery, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Hjardarhagi 4, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik, Iceland
| |
Collapse
|
11
|
Kalayinia S, Maleki M, Rokni-Zadeh H, Changi-Ashtiani M, Ahangar H, Biglari A, Shahani T, Mahdieh N. GATA4 screening in Iranian patients of various ethnicities affected with congenital heart disease: Co-occurrence of a novel de novo translocation (5;7) and a likely pathogenic heterozygous GATA4 mutation in a family with autosomal dominant congenital heart disease. J Clin Lab Anal 2019; 33:e22923. [PMID: 31115957 PMCID: PMC6757118 DOI: 10.1002/jcla.22923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/20/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common birth defect and a major health problem around the world. However, its exact etiology has remained unclear. Among various genetic contributing factors, GATA4 transcription factor plays a significant role in the CHD pathogenesis. In this study, GATA4 coding sequence was screened in Iranian patients of various ethnicities. METHODS Sixty six individuals with familial CHD referred to our center were recruited in this study. After receiving written informed consent from each individual or their parents, chromosomal analyses and GATA4 variant screening were performed. Pathogenicity of the suspected variants was evaluated using available online software tools: CADD, Mutation Taster, SIFT, and PolyPhen-2. RESULTS A total of twelve GATA4 variants were detected including five intronic, 2 exonic and 3 polymorphisms as well as 2 missense mutations, the c.1220C>A and c.1309G>A. Unlike the c.1220C>A, the likely pathogenic heterozygous c.1309G>A has not been previously associated with any phenotype. Here, we not only report, for the first time, a c.1309G>A-related CHD, but also report a novel de novo balanced translocation, 46,XY,t(5;7)(qter13;qter11), in the same patient which may have influenced the disease severity. CONCLUSION From screening GATA4 sequence in 66 Iranian patients of various ethnicities, we conclude that cytogenetic analysis and PCR-direct sequencing of different candidate genes may not be the best approach for genetic diagnosis in CHD. Applying novel approaches such as next-generation sequencing (NGS) may provide a better understating of genetic contributing factors in CHD patients for whom conventional methods could not reveal any genetic causative factor.
Collapse
Affiliation(s)
- Samira Kalayinia
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran.,Cardiogenetics Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetics Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hassan Rokni-Zadeh
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Majid Changi-Ashtiani
- School of Mathematics, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Hassan Ahangar
- Department of Cardiology, Mousavi Hospital, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran.,Department of Cardiology, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Alireza Biglari
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Tina Shahani
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Nejat Mahdieh
- Cardiogenetics Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
12
|
Martin LJ, Pilipenko V, Benson DW. Role of Segregation for Variant Discovery in Multiplex Families Ascertained by Probands With Left Sided Cardiovascular Malformations. Front Genet 2019; 9:729. [PMID: 30687393 PMCID: PMC6336695 DOI: 10.3389/fgene.2018.00729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/22/2018] [Indexed: 12/31/2022] Open
Abstract
Cardiovascular malformations (CVM) are common birth defects (incidence of 2-5/100 live births). Although a genetic basis is established, in most cases the cause remains unknown. Analysis of whole exome sequencing (WES) in left sided CVM case and trio series has identified large numbers of potential variants but evidence of causality has remained elusive except in a small percentage of cases. We sought to determine whether variant segregation in families would aid in novel gene discovery. The objective was to compare conventional and co-segregation approaches for WES in multiplex families. WES was performed on 52 individuals from 4 multiplex families ascertained by probands with hypoplastic left heart syndrome (HLHS). We identified rare variants with informatics support (RVIS, minor allele frequency ≤0.01 and Combined Annotation Dependent Depletion score ≥20) in probands. Non-RVIS variants did not meet these criteria. Family specific two point logarithm of the odds (LOD) scores identified co-segregating variants (C-SV) using a dominant model and 80% penetrance. In families, 702 RVIS in 668 genes were identified, but only 1 RVIS was also a C-SV (LOD ≥ 1). On the other hand, there were 109 non-RVIS variants with LOD ≥ 1. Among 110 C-SV, 97% were common (MAF > 1%). These results suggest that conventional variant identification methods focused on RVIS, miss most C-SV. For diseases such as left sided CVM, which exhibit strong familial transmission, co-segregation can identify novel candidates.
Collapse
Affiliation(s)
- Lisa J Martin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, United States
| | - Valentina Pilipenko
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - D Woodrow Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| |
Collapse
|
13
|
Stiller B, Schunkert H. Fifty generations of Icelanders help to explain a cause of aortic coarctation. Eur Heart J 2018; 39:3250-3252. [PMID: 29697798 DOI: 10.1093/eurheartj/ehy230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Barbara Stiller
- Deutsches Herzzentrum München, Lazarettstrasse 36, Munich, Germany.,Technische Universität München, Munich, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Lazarettstrasse 36, Munich, Germany.,Technische Universität München, Munich, Germany.,Deutsches Zentrum für Herz- und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| |
Collapse
|
14
|
Mercer CL, Andreoletti G, Carroll A, Salmon AP, Temple IK, Ennis S. Familial Ebstein Anomaly: Whole Exome Sequencing Identifies Novel Phenotype Associated With FLNA. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.116.001683. [PMID: 29237676 DOI: 10.1161/circgenetics.116.001683] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/20/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Familial Ebstein anomaly is a rare form of congenital heart disease. We report 7 individuals among 2 generations of 1 family with Ebstein anomaly. This family was first reported in 1991 by Balaji et al in which family members were also reported to have a mild skeletal phenotype. The most likely mechanism of inheritance was concluded to be autosomal dominant. We sought to identify the genetic pathogenesis in this family using a next generation sequencing approach. METHODS AND RESULTS Whole exome sequencing was performed in 2 cousins in this family using the Agilent SureSelect Human all Exon 51 Mb version 5 capture kit. Data were processed through an analytic in-house pipeline. Whole exome sequencing identified a missense mutation in FLNA (Filamin A), an actin-binding protein located at Xq28, mutations in which are associated with the skeletal phenotypes Frontometaphyseal dysplasia, Otopalatodigital, and Melnick-Needles syndrome, with X-linked periventricular nodular heterotopia and FG syndrome (Omim, 305450). Review of the phenotypes of those with the mutation in this family shows increased severity of the cardiac phenotype and associated skeletal features in affected males, consistent with X-linked inheritance. CONCLUSIONS Although congenital heart disease is reported in families with mutations in FLNA, this is the first report of individuals being affected by Ebstein anomaly because of a mutation in this gene and details the concurrent skeletal phenotype observed in this family.
Collapse
Affiliation(s)
- Catherine L Mercer
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.).
| | - Gaia Andreoletti
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.).
| | - Aisling Carroll
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
| | - Anthony P Salmon
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
| | - I Karen Temple
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
| | - Sarah Ennis
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
| |
Collapse
|
15
|
Feng Y, Hong Y, Zhang X, Cao C, Yang X, Lai S, Fan C, Cheng F, Yan M, Li C, Huang W, Chen W, Zhu P, Zeng C. Genetic variants of TREML2 are associated with HLA-B27-positive ankylosing spondylitis. Gene 2018; 668:121-128. [PMID: 29778423 DOI: 10.1016/j.gene.2018.05.057] [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: 01/24/2018] [Revised: 04/08/2018] [Accepted: 05/16/2018] [Indexed: 01/09/2023]
Abstract
Although ankylosing spondylitis (AS) is a common, highly heritable arthropathy, the precise genetic mechanism underlying the disease remains elusive. Here, we investigate the disease-causing mutations in a large AS family with distinguished complexity, consisting of 23 patients covering four generations and exhibiting a mixed HLA-B27 (+) and (-) status. Linkage analysis with 32 members using three methods and whole-exome sequencing analysis with three HLA-B27 (+) patients, one HLA-B27 (-) patient, and one healthy individual did not identify a mutation common to all of the patients, strongly suggesting the existence of genetic heterogeneity in this large pedigree. However, if only B27-positive patients were analyzed, the linkage analysis located a 22-Mb region harboring the HLA gene cluster in chromosome 6 (LOD = 4.2), and the subsequent exome analysis identified two non-synonymous mutations in the TREML2 and IP6K3 genes. These genes were resequenced among 370 sporadic AS patients and 487 healthy individuals. A significantly higher mutation frequency of TREML2 was observed in AS patients (1.51% versus 0.21%). The results obtained for the AS pedigree and sporadic patients suggest that mutation of TREML2 is a major factor leading to AS for HLA-B27 (+) members in this large family and that TREML2 is also a susceptibility gene promoting the development of ankylosing spondylitis in HLA-B27 (+) individuals.
Collapse
Affiliation(s)
- Yuan Feng
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi Province, China
| | - Yaqiang Hong
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhang
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi Province, China
| | - Chunwei Cao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xichao Yang
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi Province, China
| | - Shujuan Lai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chunmei Fan
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi Province, China
| | - Feng Cheng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Mei Yan
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi Province, China
| | - Chaohua Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Wan Huang
- Department of Cell Biology, Fourth Military Medical University, Xi'an, Shanxi Province, China
| | - Wei Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ping Zhu
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi Province, China.
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Collaborative Innovation Center for Genetics and Development, Shanghai, China.
| |
Collapse
|
16
|
Kalayinia S, Goodarzynejad H, Maleki M, Mahdieh N. Next generation sequencing applications for cardiovascular disease. Ann Med 2018; 50:91-109. [PMID: 29027470 DOI: 10.1080/07853890.2017.1392595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs). Finding new variants may contribute to establishing a risk profile for the pathology process of diseases. Here, recent applications of NGS in cardiovascular medicine are discussed; both Mendelian disorders of the cardiovascular system and complex genetic CVDs including inherited cardiomyopathy, channelopathies, stroke, coronary artery disease (CAD) and are considered. We also state some future use of NGS in clinical practice for increasing our information about the CVDs genetics and the limitations of this new technology. Key messages Traditional Sanger's method was the mainstay for Human Genome Project (HGP); Sanger sequencing has high fidelity but is slow and costly as compared to next generation methods. Within cardiovascular medicine, NGS has been shown to be successful in identifying novel causative mutations and in the diagnosis of Mendelian diseases which are caused by a single variant in a single gene. NGS has provided the opportunity to perform parallel analysis of a great number of genes in an unbiased approach (i.e. without knowing the underlying biological mechanism) which probably contribute to advance our knowledge regarding the pathology of complex diseases such as CVD.
Collapse
Affiliation(s)
- Samira Kalayinia
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | | | - Majid Maleki
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | - Nejat Mahdieh
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Hinton RB, Ware SM. Heart Failure in Pediatric Patients With Congenital Heart Disease. Circ Res 2017; 120:978-994. [PMID: 28302743 DOI: 10.1161/circresaha.116.308996] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 12/14/2022]
Abstract
Heart failure (HF) is a complex clinical syndrome resulting from diverse primary and secondary causes and shared pathways of disease progression, correlating with substantial mortality, morbidity, and cost. HF in children is most commonly attributable to coexistent congenital heart disease, with different risks depending on the specific type of malformation. Current management and therapy for HF in children are extrapolated from treatment approaches in adults. This review discusses the causes, epidemiology, and manifestations of HF in children with congenital heart disease and presents the clinical, genetic, and molecular characteristics that are similar or distinct from adult HF. The objective of this review is to provide a framework for understanding rapidly increasing genetic and molecular information in the challenging context of detailed phenotyping. We review clinical and translational research studies of HF in congenital heart disease including at the genome, transcriptome, and epigenetic levels. Unresolved issues and directions for future study are presented.
Collapse
Affiliation(s)
- Robert B Hinton
- From the Department of Pediatrics and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis
| | - Stephanie M Ware
- From the Department of Pediatrics and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis.
| |
Collapse
|
19
|
Abstract
Genetic and environmental factors may be similar in certain CHD. It has been widely accepted that it is the cumulative effect of these risk factors that results in disease. Pulmonary atresia is a rare type of complex cyanotic CHD with a poor prognosis. Understanding the molecular mechanism of pulmonary atresia is essential for future diagnosis, prevention, and therapeutic approaches. In this article, we reviewed several related copy number variants and related genetic mutations, which were identified in patients with pulmonary atresia, including pulmonary atresia with ventricular septal defect and pulmonary atresia with intact ventricular septum.
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Tomita-Mitchell A, Stamm KD, Mahnke DK, Kim MS, Hidestrand PM, Liang HL, Goetsch MA, Hidestrand M, Simpson P, Pelech AN, Tweddell JS, Benson DW, Lough JW, Mitchell ME. Impact of MYH6 variants in hypoplastic left heart syndrome. Physiol Genomics 2016; 48:912-921. [PMID: 27789736 PMCID: PMC5206387 DOI: 10.1152/physiolgenomics.00091.2016] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/04/2016] [Indexed: 01/16/2023] Open
Abstract
Hypoplastic left heart syndrome (HLHS) is a clinically and anatomically severe form of congenital heart disease (CHD). Although prior studies suggest that HLHS has a complex genetic inheritance, its etiology remains largely unknown. The goal of this study was to characterize a risk gene in HLHS and its effect on HLHS etiology and outcome. We performed next-generation sequencing on a multigenerational family with a high prevalence of CHD/HLHS, identifying a rare variant in the α-myosin heavy chain (MYH6) gene. A case-control study of 190 unrelated HLHS subjects was then performed and compared with the 1000 Genomes Project. Damaging MYH6 variants, including novel, missense, in-frame deletion, premature stop, de novo, and compound heterozygous variants, were significantly enriched in HLHS cases (P < 1 × 10−5). Clinical outcomes analysis showed reduced transplant-free survival in HLHS subjects with damaging MYH6 variants (P < 1 × 10−2). Transcriptome and protein expression analyses with cardiac tissue revealed differential expression of cardiac contractility genes, notably upregulation of the β-myosin heavy chain (MYH7) gene in subjects with MYH6 variants (P < 1 × 10−3). We subsequently used patient-specific induced pluripotent stem cells (iPSCs) to model HLHS in vitro. Early stages of in vitro cardiomyogenesis in iPSCs derived from two unrelated HLHS families mimicked the increased expression of MYH7 observed in vivo (P < 1 × 10−2), while revealing defective cardiomyogenic differentiation. Rare, damaging variants in MYH6 are enriched in HLHS, affect molecular expression of contractility genes, and are predictive of poor outcome. These findings indicate that the etiology of MYH6-associated HLHS can be informed using iPSCs and suggest utility in future clinical applications.
Collapse
Affiliation(s)
- Aoy Tomita-Mitchell
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin;
| | - Karl D Stamm
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, Wisconsin
| | - Donna K Mahnke
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Min-Su Kim
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Pip M Hidestrand
- Department of Pediatric Cardiology, Eastern Maine Medical Center, Bangor, Maine
| | - Huan Ling Liang
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary A Goetsch
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mats Hidestrand
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Pippa Simpson
- Department of Pediatrics, and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Andrew N Pelech
- Department of Pediatrics, Division of Pediatric Cardiology, Pediatric Heart Center, UC Davis Children's Hospital, Sacramento, California; and
| | - James S Tweddell
- Department of Cardiothoracic Surgery, the Heart Institute, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - D Woodrow Benson
- Department of Pediatrics, and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - John W Lough
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin Milwaukee, Wisconsin
| | - Michael E Mitchell
- Department of Surgery, Division of Cardiovascular Surgery and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| |
Collapse
|
22
|
Preuss C, Capredon M, Wünnemann F, Chetaille P, Prince A, Godard B, Leclerc S, Sobreira N, Ling H, Awadalla P, Thibeault M, Khairy P, Samuels ME, Andelfinger G. Family Based Whole Exome Sequencing Reveals the Multifaceted Role of Notch Signaling in Congenital Heart Disease. PLoS Genet 2016; 12:e1006335. [PMID: 27760138 PMCID: PMC5070860 DOI: 10.1371/journal.pgen.1006335] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/31/2016] [Indexed: 11/23/2022] Open
Abstract
Left-ventricular outflow tract obstructions (LVOTO) encompass a wide spectrum of phenotypically heterogeneous heart malformations which frequently cluster in families. We performed family based whole-exome and targeted re-sequencing on 182 individuals from 51 families with multiple affected members. Central to our approach is the family unit which serves as a reference to identify causal genotype-phenotype correlations. Screening a multitude of 10 overlapping phenotypes revealed disease associated and co-segregating variants in 12 families. These rare or novel protein altering mutations cluster predominantly in genes (NOTCH1, ARHGAP31, MAML1, SMARCA4, JARID2, JAG1) along the Notch signaling cascade. This is in line with a significant enrichment (Wilcoxon, p< 0.05) of variants with a higher pathogenicity in the Notch signaling pathway in patients compared to controls. The significant enrichment of novel protein truncating and missense mutations in NOTCH1 highlights the allelic and phenotypic heterogeneity in our pediatric cohort. We identified novel co-segregating pathogenic mutations in NOTCH1 associated with left and right-sided cardiac malformations in three independent families with a total of 15 affected individuals. In summary, our results suggest that a small but highly pathogenic fraction of family specific mutations along the Notch cascade are a common cause of LVOTO. Left-ventricular outflow tract obstructions comprise a group of developmental heart disorders that are genetically and phenotypically heterogeneous, with no single gene accounting for the majority of cases. In order to identify mutations contributing to disease, we selected patients from 51 families with a history of congenital cardiac malformations. We interrogated the entire coding sequences of 106 patients and identified a small but highly pathogenic fraction of mutations that are likely to contribute to disease in 12 families (23.5%). Furthermore, we present a strategy for identifying candidate mutations based on familial segregation in a genetically heterogeneous disorder.
Collapse
Affiliation(s)
- Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Melanie Capredon
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Florian Wünnemann
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- Faculty of Biology, University of Muenster, Muenster, Germany
| | - Philippe Chetaille
- Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l'Université (CHU) de Québec, Quebec City, Québec, Canada
| | - Andrea Prince
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Beatrice Godard
- Omics-Ethics Research Group, Research Institute of Public Health, Université de Montréal, Montréal Québec, Canada
| | - Severine Leclerc
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Nara Sobreira
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hua Ling
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Maryse Thibeault
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
| | - Paul Khairy
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | | | - Mark E. Samuels
- Centre de Recherche CHU Sainte Justine, Université de Montreal, Montréal, Québec, Canada
- Department of Medicine, Université de Montreal, Montréal, Québec, Canada
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, Québec, Canada
- * E-mail:
| |
Collapse
|
23
|
Landis BJ, Ware SM. The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges. Front Cardiovasc Med 2016; 3:22. [PMID: 27504451 PMCID: PMC4959014 DOI: 10.3389/fcvm.2016.00022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Human cardiovascular malformations (CVMs) frequently have a genetic contribution. Through the application of novel technologies, such as next-generation sequencing, DNA sequence variants associated with CVMs are being identified at a rapid pace. While clinicians are now able to offer testing with NGS gene panels or whole exome sequencing to any patient with a CVM, the interpretation of genetic variation remains problematic. Variable phenotypic expression, reduced penetrance, inconsistent phenotyping methods, and the lack of high-throughput functional testing of variants contribute to these challenges. This article elaborates critical issues that impact the decision to broadly implement clinical molecular genetic testing in CVMs. Major benefits of testing include establishing a genetic diagnosis, facilitating cost-effective screening of family members who may have subclinical disease, predicting recurrence risk in offsprings, enabling early diagnosis and anticipatory management of CV and non-CV disease phenotypes, predicting long-term outcomes, and facilitating the development of novel therapies aimed at disease improvement or prevention. Limitations include financial cost, psychosocial cost, and ambiguity of interpretation of results. Multiplex families and patients with syndromic features are two groups where disease causation could potentially be firmly established. However, these account for the minority of the overall CVM population, and there is increasing recognition that genotypes previously associated with syndromes also exist in patients who lack non-CV findings. In all circumstances, ongoing dialog between cardiologists and clinical geneticists will be needed to accurately interpret genetic testing and improve these patients’ health. This may be most effectively implemented by the creation and support of CV genetics services at centers committed to pursuing testing for patients.
Collapse
Affiliation(s)
- Benjamin J Landis
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephanie M Ware
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| |
Collapse
|
24
|
LaHaye S, Corsmeier D, Basu M, Bowman JL, Fitzgerald-Butt S, Zender G, Bosse K, McBride KL, White P, Garg V. Utilization of Whole Exome Sequencing to Identify Causative Mutations in Familial Congenital Heart Disease. ACTA ACUST UNITED AC 2016; 9:320-9. [PMID: 27418595 DOI: 10.1161/circgenetics.115.001324] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 06/27/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common type of birth defect with family- and population-based studies supporting a strong genetic cause for CHD. The goal of this study was to determine whether a whole exome sequencing (WES) approach could identify pathogenic-segregating variants in multiplex CHD families. METHODS AND RESULTS WES was performed on 9 kindreds with familial CHD, 4 with atrial septal defects, 2 with patent ductus arteriosus, 2 with tetralogy of Fallot, and 1 with pulmonary valve dysplasia. Rare variants (<1% minor allele frequency) that segregated with disease were identified by WES, and variants in 69 CHD candidate genes were further analyzed. These selected variants were subjected to in silico analysis to predict pathogenicity and resulted in the discovery of likely pathogenic mutations in 3 of 9 (33%) families. A GATA4 mutation in the transactivation domain, p.G115W, was identified in familial atrial septal defects and demonstrated decreased transactivation ability in vitro. A p.I263V mutation in TLL1 was identified in an atrial septal defects kindred and is predicted to affect the enzymatic functionality of TLL1. A disease-segregating splice donor site mutation in MYH11 (c.4599+1delG) was identified in familial patent ductus arteriosus and found to disrupt normal splicing of MYH11 mRNA in the affected individual. CONCLUSIONS Our findings demonstrate the clinical utility of WES to identify causative mutations in familial CHD and demonstrate the successful use of a CHD candidate gene list to allow for a more streamlined approach enabling rapid prioritization and identification of likely pathogenic variants from large WES data sets. CLINICAL TRIAL REGISTRATION URL: https://clinicaltrials.gov; Unique Identifier: NCT0112048.
Collapse
Affiliation(s)
- Stephanie LaHaye
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Don Corsmeier
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Madhumita Basu
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Jessica L Bowman
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Sara Fitzgerald-Butt
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Gloria Zender
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Kevin Bosse
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Kim L McBride
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus
| | - Peter White
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus.
| | - Vidu Garg
- From the Center for Cardiovascular Research, The Research Institute (S.L., M.B., S.F.-B., G.Z., K.B., K.L.M., V.G.), The Heart Center (S.L., M.B., J.L.B., S.F.-B., K.L.M., V.G.), and Biomedical Genomics Core and the Center for Microbial Pathogenesis, The Research Institute (D.C., P.W.), Nationwide Children's Hospital, Columbus, OH; and Department of Molecular Genetics (S.L., V.G.) and Department of Pediatrics (J.L.B., S.F.-B., K.L.M., P.W., V.G.), The Ohio State University, Columbus.
| |
Collapse
|
25
|
Genome-Wide DNA Methylation Analysis and Epigenetic Variations Associated with Congenital Aortic Valve Stenosis (AVS). PLoS One 2016; 11:e0154010. [PMID: 27152866 PMCID: PMC4859473 DOI: 10.1371/journal.pone.0154010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 04/07/2016] [Indexed: 11/19/2022] Open
Abstract
Congenital heart defect (CHD) is the most common cause of death from congenital anomaly. Among several candidate epigenetic mechanisms, DNA methylation may play an important role in the etiology of CHDs. We conducted a genome-wide DNA methylation analysis using an Illumina Infinium 450k human methylation assay in a cohort of 24 newborns who had aortic valve stenosis (AVS), with gestational-age matched controls. The study identified significantly-altered CpG methylation at 59 sites in 52 genes in AVS subjects as compared to controls (either hypermethylated or demethylated). Gene Ontology analysis identified biological processes and functions for these genes including positive regulation of receptor-mediated endocytosis. Consistent with prior clinical data, the molecular function categories as determined using DAVID identified low-density lipoprotein receptor binding, lipoprotein receptor binding and identical protein binding to be over-represented in the AVS group. A significant epigenetic change in the APOA5 and PCSK9 genes known to be involved in AVS was also observed. A large number CpG methylation sites individually demonstrated good to excellent diagnostic accuracy for the prediction of AVS status, thus raising possibility of molecular screening markers for this disorder. Using epigenetic analysis we were able to identify genes significantly involved in the pathogenesis of AVS.
Collapse
|
26
|
Yuan Y, Chen W, Ma X, Wang H, Yan W, Huang G. Pedigree-based Analysis of Inherited and Noninherited Risk Factors of Congenital Heart Defects. Early Hum Dev 2015; 91:713-8. [PMID: 26324253 DOI: 10.1016/j.earlhumdev.2015.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 08/02/2015] [Accepted: 08/04/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Although congenital heart defect (CHD) pedigrees are rare, they are generally taken as evidence of the existence of a genetic etiologic mechanism or environmental factors common to family members, or a combination of both. Therefore, the analysis of CHD pedigrees is important for bridging the gap in our knowledge of its etiology. AIMS To assess the prevalence of CHD and evaluate the nongenetic factors in the CHD patients and healthy controls in the pedigrees. STUDY DESIGN Observational retrospective study. SUBJECTS Twenty-three CHD pedigrees were involved in the prevalence statistics; thirty-nine CHD cases and fifty-two healthy controls in the CHD pedigrees were included in the family-based noninherited factors analysis. OUTCOME MEASURES The three-degree relatives and overall CHD prevalence were calculated. Thirty-four noninherited risk factors were compared between the CHD and control groups, first by univariate analysis and later by multivariable logistic stepwise regression analysis. RESULTS The CHD prevalence of the probands' relatives in all pedigrees was 8.0%, and it was 10.9%, 2.9% and 11.9% in first-, second- and third-degree relatives, respectively. The three risk factors, including maternal febrile illnesses (OR=14.2, 95%CI: [1.5 - 133.7]), influenza (OR=6.9 [2.0 - 23.6]) and air pollution (OR=13.5 [2.6 - 70.5]), were strongly associated with a higher risk of CHD in our sample. CONCLUSIONS For the cluster and high prevalence of CHD in the collected pedigrees, our study confirms that genetic factors play a major role in the pathogenesis of CHD, while environmental factors, such as maternal febrile illnesses, influenza and air pollution, may also increase the burden of risk for CHD pathogenesis.
Collapse
Affiliation(s)
- Yuan Yuan
- Children's Hospital of Fudan University, Shanghai, China, 201102
| | - Weicheng Chen
- Children's Hospital of Fudan University, Shanghai, China, 201102
| | - Xiaojing Ma
- Children's Hospital of Fudan University, Shanghai, China, 201102; Shanghai Key Laboratory of Birth Defects, Shanghai, China, 201102
| | - Huijun Wang
- Children's Hospital of Fudan University, Shanghai, China, 201102; Shanghai Key Laboratory of Birth Defects, Shanghai, China, 201102
| | - Weili Yan
- Children's Hospital of Fudan University, Shanghai, China, 201102; Shanghai Key Laboratory of Birth Defects, Shanghai, China, 201102
| | - Guoying Huang
- Children's Hospital of Fudan University, Shanghai, China, 201102; Shanghai Key Laboratory of Birth Defects, Shanghai, China, 201102.
| |
Collapse
|
27
|
Bowles NE, Jou CJ, Arrington CB, Kennedy BJ, Earl A, Matsunami N, Meyers LL, Etheridge SP, Saarel EV, Bleyl SB, Yost HJ, Yandell M, Leppert MF, Tristani-Firouzi M, Gruber PJ. Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus. Am J Med Genet A 2015; 167A:2975-84. [PMID: 26284702 DOI: 10.1002/ajmg.a.37297] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/06/2015] [Indexed: 12/30/2022]
Abstract
Wolff-Parkinson-White (WPW) syndrome is a common cause of supraventricular tachycardia that carries a risk of sudden cardiac death. To date, mutations in only one gene, PRKAG2, which encodes the 5'-AMP-activated protein kinase subunit γ-2, have been identified as causative for WPW. DNA samples from five members of a family with WPW were analyzed by exome sequencing. We applied recently designed prioritization strategies (VAAST/pedigree VAAST) coupled with an ontology-based algorithm (Phevor) that reduced the number of potentially damaging variants to 10: a variant in KCNE2 previously associated with Long QT syndrome was also identified. Of these 11 variants, only MYH6 p.E1885K segregated with the WPW phenotype in all affected individuals and was absent in 10 unaffected family members. This variant was predicted to be damaging by in silico methods and is not present in the 1,000 genome and NHLBI exome sequencing project databases. Screening of a replication cohort of 47 unrelated WPW patients did not identify other likely causative variants in PRKAG2 or MYH6. MYH6 variants have been identified in patients with atrial septal defects, cardiomyopathies, and sick sinus syndrome. Our data highlight the pleiotropic nature of phenotypes associated with defects in this gene.
Collapse
Affiliation(s)
- Neil E Bowles
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Chuanchau J Jou
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah.,Nora Eccles Cardiovascular Research and Training Institute, Salt Lake City, Utah
| | - Cammon B Arrington
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Brett J Kennedy
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Aubree Earl
- Department of Cardiothoracic Surgery, University of Utah School of Medicine, Salt Lake City, Utah
| | - Norisada Matsunami
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lindsay L Meyers
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Susan P Etheridge
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Elizabeth V Saarel
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Steven B Bleyl
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah.,Clinical Genetics Institute, Intermountain Healthcare, Salt Lake City, Utah
| | - H Joseph Yost
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Mark Yandell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah.,USTAR Center for Genetic Discovery, University of Iowa, Iowa City, Iowa
| | - Mark F Leppert
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Martin Tristani-Firouzi
- Department of Pediatrics, Division of Cardiology, University of Utah School of Medicine, Salt Lake City, Utah.,Nora Eccles Cardiovascular Research and Training Institute, Salt Lake City, Utah
| | - Peter J Gruber
- Department of Cardiothoracic Surgery, University of Utah School of Medicine, Salt Lake City, Utah.,Department of Cardiothoracic Surgery, University of Iowa, Iowa City, Iowa
| | | |
Collapse
|
28
|
Theis JL, Zimmermann MT, Evans JM, Eckloff BW, Wieben ED, Qureshi MY, O’Leary PW, Olson TM. Recessive
MYH6
Mutations in Hypoplastic Left Heart With Reduced Ejection Fraction. ACTA ACUST UNITED AC 2015; 8:564-71. [DOI: 10.1161/circgenetics.115.001070] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/09/2015] [Indexed: 12/28/2022]
Abstract
Background—
The molecular underpinnings of hypoplastic left heart are poorly understood. Staged surgical palliation has dramatically improved survival, yet eventual failure of the systemic right ventricle necessitates cardiac transplantation in a subset of patients. We sought to identify genetic determinants of hypoplastic left heart with latent right ventricular dysfunction in individuals with a Fontan circulation.
Methods and Results—
Evaluation of cardiac structure and function by echocardiography in patients with hypoplastic left heart and their first-degree relatives identified 5 individuals with right ventricular ejection fraction ≤40% after Fontan operation. Whole genome sequencing was performed on DNA from 21 family members, filtering for genetic variants with allele frequency <1% predicted to alter protein structure or expression. Secondary family-based filtering for de novo and recessive variants revealed rare inherited missense mutations on both paternal and maternal alleles of
MYH6
, encoding myosin heavy chain 6, in 2 patients who developed right ventricular dysfunction 3 to 11 years postoperatively. Parents and siblings who were heterozygous carriers had normal echocardiograms. Protein modeling of the 4 highly conserved amino acid substitutions, residing in both head and tail domains, predicted perturbation of protein structure and function.
Conclusions—
In contrast to dominant
MYH6
mutations with variable penetrance identified in other congenital heart defects and dilated cardiomyopathy, this study reveals compound heterozygosity for recessive
MYH6
mutations in patients with hypoplastic left heart and reduced systemic right ventricular ejection fraction. These findings implicate a shared molecular basis for the developmental arrest and latent myopathy of left and right ventricles, respectively.
Collapse
Affiliation(s)
- Jeanne L. Theis
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| | - Michael T. Zimmermann
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| | - Jared M. Evans
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| | - Bruce W. Eckloff
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| | - Eric D. Wieben
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| | - Muhammad Y. Qureshi
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| | - Patrick W. O’Leary
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| | - Timothy M. Olson
- From the Cardiovascular Genetics Research Laboratory (J.L.T., T.M.O.), Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine (M.Y.Q., P.W.O’L., T.M.O.), Division of Cardiovascular Diseases, Department of Internal Medicine (T.M.O.), Departments of Health Sciences Research and Biomedical Statistics and Informatics (M.T.Z., J.M.E.), Medical Genome Facility (B.W.E., E.D.W.), and Department of Biochemistry and Molecular Biology (E.D.W.), Mayo Clinic, Rochester, MN
| |
Collapse
|
29
|
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.
Collapse
|
30
|
Abstract
Congenital heart defects (CHDs) are structural abnormalities of the heart and great vessels that are present from birth. The presence or absence of extracardiac anomalies has historically been used to identify patients with possible monogenic, chromosomal, or teratogenic CHD causes. These distinctions remain clinically relevant, but it is increasingly clear that nonsyndromic CHDs can also be genetic. This article discusses key morphologic, molecular, and signaling mechanisms relevant to heart development, summarizes overall progress in molecular genetic analyses of CHDs, and provides current recommendations for clinical application of genetic testing.
Collapse
Affiliation(s)
- Jason R Cowan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics and Medical and Molecular Genetics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Indianapolis, IN 46202, USA
| | - Stephanie M Ware
- Department of Pediatrics and Medical and Molecular Genetics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Indianapolis, IN 46202, USA.
| |
Collapse
|
31
|
Webber DM, MacLeod SL, Bamshad MJ, Shaw GM, Finnell RH, Shete SS, Witte JS, Erickson SW, Murphy LD, Hobbs C. Developments in our understanding of the genetic basis of birth defects. ACTA ACUST UNITED AC 2015; 103:680-91. [PMID: 26033863 DOI: 10.1002/bdra.23385] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Birth defects are a major cause of morbidity and mortality worldwide. There has been much progress in understanding the genetic basis of familial and syndromic forms of birth defects. However, the etiology of nonsydromic birth defects is not well-understood. Although there is still much work to be done, we have many of the tools needed to accomplish the task. Advances in next-generation sequencing have introduced a sea of possibilities, from disease-gene discovery to clinical screening and diagnosis. These advances have been fruitful in identifying a host of candidate disease genes, spanning the spectrum of birth defects. With the advent of CRISPR-Cas9 gene editing, researchers now have a precise tool for characterizing this genetic variation in model systems. Work in model organisms has also illustrated the importance of epigenetics in human development and birth defects etiology. Here we review past and current knowledge in birth defects genetics. We describe genotyping and sequencing methods for the detection and analysis of rare and common variants. We remark on the utility of model organisms and explore epigenetics in the context of structural malformation. We conclude by highlighting approaches that may provide insight into the complex genetics of birth defects.
Collapse
Affiliation(s)
- Daniel M Webber
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Stewart L MacLeod
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Michael J Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Gary M Shaw
- Stanford University School of Medicine, Stanford, California
| | - Richard H Finnell
- Dell Pediatric Research Institute, Department of Nutritional Sciences, The University of Texas at Austin, Austin, Texas
| | - Sanjay S Shete
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Stephen W Erickson
- Department of Biostatistics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Linda D Murphy
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Charlotte Hobbs
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| |
Collapse
|
32
|
Hinton RB, McBride KL, Bleyl SB, Bowles NE, Border WL, Garg V, Smolarek TA, Lalani SR, Ware SM. Rationale for the Cytogenomics of Cardiovascular Malformations Consortium: A Phenotype Intensive Registry Based Approach. J Cardiovasc Dev Dis 2015; 2:76-92. [PMID: 29371513 PMCID: PMC5753096 DOI: 10.3390/jcdd2020076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 04/18/2015] [Accepted: 04/22/2015] [Indexed: 12/23/2022] Open
Abstract
Cardiovascular malformations (CVMs) are the most common birth defect, occurring in 1%–5% of all live births. Although the genetic contribution to CVMs is well recognized, the genetic causes of human CVMs are identified infrequently. In addition, a failure of systematic deep phenotyping of CVMs, resulting from the complexity and heterogeneity of malformations, has obscured genotype-phenotype correlations and contributed to a lack of understanding of disease mechanisms. To address these knowledge gaps, we have developed the Cytogenomics of Cardiovascular Malformations (CCVM) Consortium, a multi-site alliance of geneticists and cardiologists, contributing to a database registry of submicroscopic genetic copy number variants (CNVs) based on clinical chromosome microarray testing in individuals with CVMs using detailed classification schemes. Cardiac classification is performed using a modification to the National Birth Defects Prevention Study approach, and non-cardiac diagnoses are captured through ICD-9 and ICD-10 codes. By combining a comprehensive approach to clinically relevant genetic analyses with precise phenotyping, the Consortium goal is to identify novel genomic regions that cause or increase susceptibility to CVMs and to correlate the findings with clinical phenotype. This registry will provide critical insights into genetic architecture, facilitate genotype-phenotype correlations, and provide a valuable resource for the medical community.
Collapse
Affiliation(s)
- Robert B Hinton
- Divisions of Cardiology and Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Kim L McBride
- Center for Cardiovascular and Pulmonary Research and Heart Center, Nationwide Children's Hospital and Department of Pediatrics, Ohio State University, Columbus, OH 43205, USA.
| | - Steven B Bleyl
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - Neil E Bowles
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
| | - William L Border
- Division of Cardiology, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
| | - Vidu Garg
- Center for Cardiovascular and Pulmonary Research and Heart Center, Nationwide Children's Hospital and Department of Pediatrics, Ohio State University, Columbus, OH 43205, USA.
| | - Teresa A Smolarek
- Divisions of Cardiology and Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Stephanie M Ware
- Departments of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| |
Collapse
|
33
|
Ishikawa T, Jou CJ, Nogami A, Kowase S, Arrington CB, Barnett SM, Harrell DT, Arimura T, Tsuji Y, Kimura A, Makita N. Novel mutation in the α-myosin heavy chain gene is associated with sick sinus syndrome. Circ Arrhythm Electrophysiol 2015; 8:400-8. [PMID: 25717017 DOI: 10.1161/circep.114.002534] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/11/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Recent genome-wide association studies have demonstrated an association between MYH6, the gene encoding α-myosin heavy chain (α-MHC), and sinus node function in the general population. Moreover, a rare MYH6 variant, R721W, predisposing susceptibility to sick sinus syndrome has been identified. However, the existence of disease-causing MYH6 mutations for familial sick sinus syndrome and their underlying mechanisms remain unknown. METHODS AND RESULTS We screened 9 genotype-negative probands with sick sinus syndrome families for mutations in MYH6 and identified an in-frame 3-bp deletion predicted to delete one residue (delE933) at the highly conserved coiled-coil structure within the binding motif to myosin-binding protein C in one patient. Co-immunoprecipitation analysis revealed enhanced binding of delE933 α-MHC to myosin-binding protein C. Irregular fluorescent speckles retained in the cytoplasm with substantially disrupted sarcomere striation were observed in neonatal rat cardiomyocytes transfected with α-MHC mutants carrying delE933 or R721W. In addition to the sarcomere impairments, delE933 α-MHC exhibited electrophysiological abnormalities both in vitro and in vivo. The atrial cardiomyocyte cell line HL-1 stably expressing delE933 α-MHC showed a significantly slower conduction velocity on multielectrode array than those of wild-type α-MHC or control plasmid transfected cells. Furthermore, targeted morpholino knockdown of MYH6 in zebrafish significantly reduced the heart rate, which was rescued by coexpressed wild-type human α-MHC but not by delE933 α-MHC. CONCLUSIONS The novel MYH6 mutation delE933 causes both structural damage of the sarcomere and functional impairments on atrial action propagation. This report reinforces the relevance of MYH6 for sinus node function and identifies a novel pathophysiology underlying familial sick sinus syndrome.
Collapse
Affiliation(s)
- Taisuke Ishikawa
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Chuanchau J Jou
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Akihiko Nogami
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Shinya Kowase
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Cammon B Arrington
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Spencer M Barnett
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Daniel T Harrell
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Takuro Arimura
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Yukiomi Tsuji
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.)
| | - Akinori Kimura
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.).
| | - Naomasa Makita
- From the Department of Molecular Physiology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki (T.I., D.T.H., Y.T., N.M.); Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan (T.I., T.A., A.K.); Division of Pediatric Cardiology, University of Utah, Salt Lake City (C.J.J., C.B.A., S.M.B.); Cardiovascular Division, University of Tsukuba, Tsukuba (A.N.); Department of Heart Rhythm Management, Yokohama Rosai Hospital, Yokohama (A.N., S.K.); and Department of Veterinary Medicine, Kagoshima University, Kagoshima, Japan (T.A.).
| |
Collapse
|
34
|
Blue GM, Kirk EP, Giannoulatou E, Dunwoodie SL, Ho JW, Hilton DC, White SM, Sholler GF, Harvey RP, Winlaw DS. Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Familial Congenital Heart Disease. J Am Coll Cardiol 2014; 64:2498-506. [DOI: 10.1016/j.jacc.2014.09.048] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/18/2014] [Accepted: 09/16/2014] [Indexed: 01/06/2023]
|
35
|
Krupp DR, Soldano KL, Garrett ME, Cope H, Ashley-Koch AE, Gregory SG. Missing genetic risk in neural tube defects: can exome sequencing yield an insight? ACTA ACUST UNITED AC 2014; 100:642-6. [PMID: 25044326 DOI: 10.1002/bdra.23276] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 01/12/2023]
Abstract
BACKGROUND Neural tube defects (NTD) have a strong genetic component, with up to 70% of variance in human prevalence determined by heritable factors. Although the identification of causal DNA variants by sequencing candidate genes from functionally relevant pathways and model organisms has provided some success, alternative approaches are demanded. METHODS Next generation sequencing platforms are facilitating the production of massive amounts of sequencing data, primarily from the protein coding regions of the genome, at a faster rate and cheaper cost than has previously been possible. These platforms are permitting the identification of variants (de novo, rare, and common) that are drivers of NYTD etiology, and the cost of the approach allows for the screening of increased numbers of affected and unaffected individuals from NTD families and in simplex cases. CONCLUSION The next generation sequencing platforms represent a powerful tool in the armory of the genetics researcher to identify the causal genetic basis of NTDs.
Collapse
Affiliation(s)
- Deidre R Krupp
- Duke Molecular Physiology Institute, DUMC, 300 North Duke Street, Durham, NC, 27701
| | | | | | | | | | | |
Collapse
|
36
|
Bowles NE, Arrington CB, Hirono K, Nakamura T, Ngo L, Wee YS, Ichida F, Weis JH. Kawasaki disease patients homozygous for the rs12252-C variant of interferon-induced transmembrane protein-3 are significantly more likely to develop coronary artery lesions. Mol Genet Genomic Med 2014; 2:356-61. [PMID: 25077179 PMCID: PMC4113277 DOI: 10.1002/mgg3.79] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/03/2014] [Accepted: 03/11/2014] [Indexed: 12/17/2022] Open
Affiliation(s)
- Neil E Bowles
- Division of Cardiology, Department of Pediatrics, University of Utah School of Medicine Salt Lake City, Utah
| | - Cammon B Arrington
- Division of Cardiology, Department of Pediatrics, University of Utah School of Medicine Salt Lake City, Utah
| | - Keiichi Hirono
- Department of Pediatrics, Faculty of Medicine, University of Toyama Toyama, Japan
| | | | - Long Ngo
- Department of Medicine, Harvard Medical School, Beth Israel Deaconess Medical Center Brookline, Massachusetts
| | - Yin Shen Wee
- Department of Pathology, University of Utah School of Medicine Salt Lake City, Utah
| | - Fukiko Ichida
- Department of Pediatrics, Faculty of Medicine, University of Toyama Toyama, Japan
| | - John H Weis
- Department of Pathology, University of Utah School of Medicine Salt Lake City, Utah
| |
Collapse
|
37
|
|
38
|
Xie L, Chen JL, Zhang WZ, Wang SZ, Zhao TL, Huang C, Wang J, Yang JF, Yang YF, Tan ZP. Rare de novo copy number variants in patients with congenital pulmonary atresia. PLoS One 2014; 9:e96471. [PMID: 24826987 PMCID: PMC4020819 DOI: 10.1371/journal.pone.0096471] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 04/08/2014] [Indexed: 11/18/2022] Open
Abstract
Background Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA). Methods and Results Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features. Conclusions Rare CNVs contribute to the pathogenesis of PA (9.8%), suggesting that the causes of PA are heterogeneous and pleiotropic. Together with previous data from animal models, our results might help identify a link between CHD and folate-mediated one-carbon metabolism (FOCM). With the accumulation of high-resolution SNP array data, these previously undescribed rare CNVs may help reveal critical gene(s) in CHD and may provide novel insights about CHD pathogenesis.
Collapse
MESH Headings
- Adolescent
- Case-Control Studies
- Child
- Child, Preschool
- Chromosome Aberrations
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 22
- DNA Copy Number Variations
- Female
- Folic Acid/metabolism
- Genetic Loci
- Genome-Wide Association Study
- Heart Defects, Congenital/diagnostic imaging
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/pathology
- Heart Defects, Congenital/surgery
- Humans
- Infant
- Infant, Newborn
- Male
- Oligonucleotide Array Sequence Analysis
- Pulmonary Atresia/diagnostic imaging
- Pulmonary Atresia/genetics
- Pulmonary Atresia/pathology
- Pulmonary Atresia/surgery
- Ultrasonography
- Vitamin B 12/metabolism
Collapse
Affiliation(s)
- Li Xie
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jin-Lan Chen
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Wei-Zhi Zhang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Shou-Zheng Wang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Tian-Li Zhao
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Can Huang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jian Wang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jin-Fu Yang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Yi-Feng Yang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- * E-mail: (ZPT); (YFY)
| | - Zhi-Ping Tan
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- * E-mail: (ZPT); (YFY)
| |
Collapse
|
39
|
Exome sequencing identifies a novel variant in ACTC1 associated with familial atrial septal defect. Can J Cardiol 2013; 30:181-7. [PMID: 24461919 DOI: 10.1016/j.cjca.2013.12.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/02/2013] [Accepted: 12/02/2013] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The genetics of congenital heart disease (CHD) remain incompletely understood. Exome sequencing has been successfully used to identify disease-causing mutations in familial disorders in which candidate gene analyses and linkage mapping have failed. METHODS We studied a large family characterized by autosomal dominant isolated secundum atrial septal defect (ASD) (MIM No. 612794). Candidate gene resequencing and linkage analysis were uninformative. RESULTS Whole-exome sequencing of 2 affected family members identified 44 rare shared variants, including a nonsynonymous mutation (c.532A>T, p.M178L, NM_005159.4) in alpha-cardiac actin (ACTC1). This mutation was absent from 1834 internal controls as well as from the 1000 Genomes and the Exome Sequencing Project (ESP) databases, but predictions regarding its effect on protein function were divergent. However, p.M178L was the only rare mutation segregating with disease in our family. CONCLUSIONS Our results provide further evidence supporting a causative role for ACTC1 mutations in ASD. Massively parallel sequencing of the exome allows for the detection of novel rare variants causing CHD without the limitations of a candidate gene approach. When mutation prediction algorithms are not helpful, studies of familial disease can help distinguish rare pathologic mutations from benign variants. Consideration of the family history can lead to genetic insights into CHD.
Collapse
|
40
|
Ganesh SK, Arnett DK, Assimes TL, Basson CT, Chakravarti A, Ellinor PT, Engler MB, Goldmuntz E, Herrington DM, Hershberger RE, Hong Y, Johnson JA, Kittner SJ, McDermott DA, Meschia JF, Mestroni L, O’Donnell CJ, Psaty BM, Vasan RS, Ruel M, Shen WK, Terzic A, Waldman SA. Genetics and Genomics for the Prevention and Treatment of Cardiovascular Disease: Update. Circulation 2013; 128:2813-51. [DOI: 10.1161/01.cir.0000437913.98912.1d] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
41
|
Dorn C, Grunert M, Sperling SR. Application of high-throughput sequencing for studying genomic variations in congenital heart disease. Brief Funct Genomics 2013; 13:51-65. [PMID: 24095982 DOI: 10.1093/bfgp/elt040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Congenital heart diseases (CHD) represent the most common birth defect in human. The majority of cases are caused by a combination of complex genetic alterations and environmental influences. In the past, many disease-causing mutations have been identified; however, there is still a large proportion of cardiac malformations with unknown precise origin. High-throughput sequencing technologies established during the last years offer novel opportunities to further study the genetic background underlying the disease. In this review, we provide a roadmap for designing and analyzing high-throughput sequencing studies focused on CHD, but also with general applicability to other complex diseases. The three main next-generation sequencing (NGS) platforms including their particular advantages and disadvantages are presented. To identify potentially disease-related genomic variations and genes, different filtering steps and gene prioritization strategies are discussed. In addition, available control datasets based on NGS are summarized. Finally, we provide an overview of current studies already using NGS technologies and showing that these techniques will help to further unravel the complex genetics underlying CHD.
Collapse
Affiliation(s)
- Cornelia Dorn
- Department of Cardiovascular Genetics, Experimental and Clinical Research Center (ECRC), Charité-University Medicine Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany. Department of Biochemistry, Free University Berlin, Berlin, Germany. Tel.: +49-(0)30-450540123; Fax: +49-(0)30-84131699;
| | | | | |
Collapse
|
42
|
Arrington CB, Bleyl SB, Brunelli L, Bowles NE. Family-based studies to identify genetic variants that cause congenital heart defects. Future Cardiol 2013; 9:507-18. [PMID: 23834692 DOI: 10.2217/fca.13.40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Congenital heart defects (CHDs) are the most common congenital abnormalities. Analysis of large multigenerational families has led to the identification of a number of genes for CHDs. However, identifiable variations in these genes are the cause of a small proportion of cases of CHDs, suggesting significant genetic heterogeneity. In addition, large families with CHDs are rare, making the identification of additional genes difficult. Next-generation sequencing technologies will provide an opportunity to identify more genes in the future. However, the significant genetic variation between individuals will present a challenge to distinguish between 'pathogenic' and 'benign' variants. We have demonstrated that the analysis of multiple individuals in small families using combinations of algorithms can reduce the number of candidate variants to a small, manageable number. Thus, the analysis of small nuclear families or even distantly related 'sporadic' cases may begin to uncover the 'dark matter' of CHD genetics.
Collapse
Affiliation(s)
- Cammon B Arrington
- Department of Pediatrics (Cardiology) University of Utah School of Medicine, Eccles Institute of Human Genetics, 15 North 2030 East, Room 7110B, Salt Lake City, UT 84112, USA
| | | | | | | |
Collapse
|
43
|
Preuss C, Andelfinger G. Genetics of Heart Failure in Congenital Heart Disease. Can J Cardiol 2013; 29:803-10. [DOI: 10.1016/j.cjca.2013.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/27/2013] [Accepted: 03/06/2013] [Indexed: 01/09/2023] Open
|
44
|
Fung A, Manlhiot C, Naik S, Rosenberg H, Smythe J, Lougheed J, Mondal T, Chitayat D, McCrindle BW, Mital S. Impact of prenatal risk factors on congenital heart disease in the current era. J Am Heart Assoc 2013; 2:e000064. [PMID: 23727699 PMCID: PMC3698764 DOI: 10.1161/jaha.113.000064] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background The healthcare burden related to congenital heart disease (CHD) is increasing with improving survival. We assessed changing trends in prenatal risk factors for CHD in the current era in a Canadian cohort. Methods and Results CHD patients <18 years old (n=2339) and controls without structural heart disease (n=199) were prospectively enrolled in an Ontario province‐wide biobank registry from 2008–2011. Family history, frequency of extra‐cardiac anomalies (ECAs), and antenatal risk factors were assessed. Temporal trends were analyzed and associations with CHD were measured using linear and logistic regression. Family history of CHD and frequency of major ECAs was higher in cases versus controls (P<0.001). Despite an increase in genetic testing in the recent era, only 9.5% of cases with CHD had a confirmed genetic diagnosis. Yield of genetic testing (ie, frequency of abnormal results) was higher in familial and syndromic cases. There was an increase in parental age at conception, maternal prepregnancy body mass index, maternal urinary tract infections, type 1 diabetes, and exposure to nonfertility medications during pregnancy from 1990–2011. Later year of birth, family history of CHD, presence of major ECAs, maternal smoking during pregnancy, and maternal medication exposure were associated with increased odds of CHD (P<0.05 for all). Advanced parental age was associated with increased odds of CHD caused by genetic abnormalities. Conclusions The increase in prenatal risk factors for CHD highlights the need for more rigorous ascertainment of genetic and environmental factors including gene‐environment interactions that contribute to CHD.
Collapse
Affiliation(s)
- Alan Fung
- Division of Cardiology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Circulation Research
Thematic Synopsis. Circ Res 2013. [DOI: 10.1161/circresaha.113.300982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
46
|
Abstract
PURPOSE OF REVIEW Advances in genomics have paved the way for personalized medicine applications. This review will discuss new discoveries in genomics and pharmacogenomics in children with congenital heart disease (CHD) and the application towards the development of new diagnostics, disease risk predictions, and optimizing response to drugs and surgery. RECENT FINDINGS Recent advances have identified common and rare variants associated with complex CHD using next-generation sequencing and genotyping technology. Next-generation sequencing is now being used not only for clinical genetic testing but also for noninvasive prenatal testing of fetal DNA in maternal serum to diagnose genetic conditions like fetal aneuploidies as early as the first trimester. This approach is not only more accurate but also safer than invasive maternal screening tests. This technology may also help in noninvasive diagnosis of transplant rejection. As genetic variations that influence the response to surgery in CHD are identified, this can guide decision-making surrounding optimum type and timing of surgery. Drug choice and dosing are being increasingly influenced by knowledge of pharmacogenetic and pharmacodynamic variations. Age-related and maturation-related changes in drug pharmacokinetics make it crucial to perform pediatric-targeted pharmacogenetic studies to enable the incorporation of age into genotype-guided drug dosing algorithms. SUMMARY Rapid genomic and pharmacogenomic discovery are guiding the development of more sensitive screening and diagnostic tests for CHD as well as development of safer and more effective drugs. This needs to be paralleled by the development of strategies to support rapid translation of emerging genomic knowledge to patient care.
Collapse
|
47
|
Circulation Research
Thematic Synopsis. Circ Res 2012. [DOI: 10.1161/res.0b013e31826396e8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|