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Karmegaraj B. Myxomatous degeneration of cardiac valves in a fetus with 6q25.1 (TAB2) deletion. Cardiol Young 2024; 34:459-461. [PMID: 38167265 DOI: 10.1017/s1047951123004419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Myxomatous degeneration of one or more cardiac valves has been reported in trisomy 18, Noonan, Marfan, and Ehlers-Danlos syndromes. 6q25.1 (TAB2) deletion is one of the notable causes for myxomatous degeneration of cardiac valves. Whole exome sequencing must be considered in these subsets of cases for effective prenatal counselling. A 23-week fetus presented with cardiomegaly, redundant myxomatous tricuspid, mitral valve leaflets, thickened pulmonary valve, and bicuspid aortic valves detected to have 6q25.1 (TAB2) deletion was presented with literature review.
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Affiliation(s)
- Balaganesh Karmegaraj
- Sowmi Fetal heart centre, Tirunelveli, TN, India
- Fetal cardiology Division, Department of Paediatric Cardiology, Amrita institute of Medical Sciences and research centre, Kochi, KL, India
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粟 闵, 李 芝, 宋 雅, 王 艳, 周 斌, 李 琴. [Association Between TAB2 Gene Polymorphisms and Susceptibility to Cryptorchidism in Han Chinese Population in Southwest China]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2022; 53:642-648. [PMID: 35871735 PMCID: PMC10409459 DOI: 10.12182/20220760209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 06/15/2023]
Abstract
Objective To conduct preliminary investigation into the correlation between transforming growth factor beta-activated protein kinase 1-binding protein 2 ( TAB2) gene and the incidence of cryptorchidism in Han Chinese population in Southwest China. Methods A total of 259 patients with cryptorchidism and 355 healthy controls from Southwest China were enrolled for the study. Polymerase chain reaction-restriction fragment length polymorphism method was used to analyze the genotype of the 3 tag single nucleotide polymorphisms (SNPs) of TAB2 gene, i.e., rs237028, rs521845 and rs652921. The Chi-square test was used to analyze the relationship between the genotype frequency of the three tag SNPs and the incidence of cryptorchidism. Results The distribution of the 3 tag SNPs' alleles and genotypes were in agreement with the Hardy-Weinberg equilibrium, and the genotype results of polymerase chain reaction-restriction fragment length polymorphism assay were consistent with those of Sanger sequencing. The frequency of the G allele at TAB 2 rs237028 was significantly higher in the cryptorchidism group than that in the control group (30.9% vs. 25.6%, P=0.04, OR=1.31, 95% CI: 1.01-1.70). In the dominant model, the risk of cryptorchidism was significantly higher in AG/GG genotype carriers ( P=0.006, OR=1.57, 95% CI: 1.14-2.17). In the cryptorchidism group, the TC/CC genotype frequency of the rs652921 locus were significantly higher than that of the control group (75.3% vs. 67.0%, P=0.03, OR=1.50, 95% CI: 1.05-2.14). Correlation between rs521845 and susceptibility to cryptorchidism was not observed in the Han Chinese population. Conclusion The AG/GG genotype of rs237028 locus and the TC/CC genotype of rs652921 locus of the TAB2 gene may be associated with increased risks of cryptorchidism in Han Chinese population in southwest China.
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Affiliation(s)
- 闵 粟
- 四川大学华西第二医院 出生缺陷与相关妇儿疾病教育部重点实验室 转化医学研究中心-分子与转化医学实验室 (成都 610041)Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - 芝隆 李
- 四川大学华西第二医院 出生缺陷与相关妇儿疾病教育部重点实验室 转化医学研究中心-分子与转化医学实验室 (成都 610041)Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - 雅平 宋
- 四川大学华西第二医院 出生缺陷与相关妇儿疾病教育部重点实验室 转化医学研究中心-分子与转化医学实验室 (成都 610041)Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - 艳云 王
- 四川大学华西第二医院 出生缺陷与相关妇儿疾病教育部重点实验室 转化医学研究中心-分子与转化医学实验室 (成都 610041)Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - 斌 周
- 四川大学华西第二医院 出生缺陷与相关妇儿疾病教育部重点实验室 转化医学研究中心-分子与转化医学实验室 (成都 610041)Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - 琴 李
- 四川大学华西第二医院 出生缺陷与相关妇儿疾病教育部重点实验室 转化医学研究中心-分子与转化医学实验室 (成都 610041)Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
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Westphal DS, Mastantuono E, Seidel H, Riedhammer KM, Hahn A, Vill K, Wagner M. There is more to it than just congenital heart defects - The phenotypic spectrum of TAB2-related syndrome. Gene 2022; 814:146167. [PMID: 34995729 DOI: 10.1016/j.gene.2021.146167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Congenital heart defects (CHD) are the most common birth defect and disease-causing variant in TAB2 have found to be associated with isolated CHD. Recently, it became evident that pathogenic, mostly loss-of-function variants in TAB2 can also cause syndromic CHD that includes connective tissue anomalies. The number of published cases is limited posing a challenge for counseling affected patients and their relatives. METHODS Cases in whom whole exome sequencing was executed at our institute between January 2015 and June 2021 were screened for disease-causing variants in TAB2. Additionally, a PubMed-based review of the literature was performed in December 2021 in order to give an updated clinical overview of the TAB2-associated phenotypic spectrum, including our cases. RESULTS We identified three cases with syndromic CHD caused by different heterozygous loss-of-function variants in TAB2. In one of these cases, the variant was inherited by a healthy father. A comparison with published cases highlights that most patients were affected by structural and/or arrhythmic heart disease (about 90%) while about two third of all cases had syndromic comorbidity especially connective tissue defects and dysmorphic abnormalities. CONCLUSION Our findings indicate a variable expressivity as well as reduced penetrance of TAB2-associated CHD. Disease-causing variants in TAB2 should be considered in cases with isolated CHD but also in syndromic CHD with connective tissue abnormalities. However, prediction of the patients' clinical outcome solely based on the variant in TAB2 is still extremely challenging.
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Affiliation(s)
- Dominik S Westphal
- Department of Internal Medicine I, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Germany; Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Germany.
| | - Elisa Mastantuono
- Department of Internal Medicine I, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Germany
| | - Heide Seidel
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Germany; Department of Congenital Heart Defects and Pediatric Cardiology, German Heart Center Munich, Technical University of Munich, Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Germany; Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Andreas Hahn
- Department of Child Neurology, Center for Rare Diseases Giessen (ZSEGI), Justus-Liebig University, Giessen, Germany
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-Universität, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Germany; Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr von Hauner Children's Hospital, LMU Hospital, Ludwig-Maximilians-Universität, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
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Abstract
PURPOSE OF REVIEW Given a general lack of emphasis on the molecular underpinnings of single ventricle (SV) congenital heart diseases (CHD), our review highlights and summarizes recent advances in uncovering the genetic and molecular mechanisms in SV CHD etiology. RECENT FINDINGS While common SV-associated genetic mutations were found in key cardiac transcription factors, other mutations were sporadic. With advances in genetic sequencing technologies and animal models, more disease-associated factors have been identified to act in critical cardiac signaling pathways such as NOTCH, Wnt, and TGF signaling. Recent studies have also revealed that different cardiac lineages play different roles in disease pathogenesis. SV defects are attributed to complex combinations of genetic mutations, indicating that sophisticated spatiotemporal regulation of gene transcription networks and functional cellular pathways govern disease progression. Future studies will warrant in-depth investigations into better understanding how different genetic factors converge to influence common downstream cellular pathways, resulting in SV abnormalities.
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Lodato V, Parlapiano G, Calì F, Silvetti MS, Adorisio R, Armando M, El Hachem M, Romanzo A, Dionisi-Vici C, Digilio MC, Novelli A, Drago F, Raponi M, Baban A. Cardiomyopathies in Children and Systemic Disorders When Is It Useful to Look beyond the Heart? J Cardiovasc Dev Dis 2022; 9:47. [PMID: 35200700 PMCID: PMC8877723 DOI: 10.3390/jcdd9020047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Cardiomyopathy (CMP) is a rare disease in the pediatric population, with a high risk of morbidity and mortality. The genetic etiology of CMPs in children is extremely heterogenous. These two factors play a major role in the difficulties of establishing standard diagnostic and therapeutic protocols. Isolated CMP in children is a frequent finding, mainly caused by sarcomeric gene variants with a detection rate that can reach up to 50% of analyzed cohorts. Complex multisystemic forms of pediatric CMP are even more heterogenous. Few studies in literature take into consideration this topic as the main core since it represents a rarity (systemic CMP) within a rarity (pediatric population CMP). Identifying etiology in this cohort is essential for understanding prognosis, risk stratification, eligibility to heart transplantation and/or mechanical-assisted procedures, preventing multiorgan complications, and relatives' recurrence risk calculation. The previous points represent a cornerstone in patients' empowerment and personalized medical care approach. The aim of this work is to propose a new approach for an algorithm in the setting of the diagnostic framework of systemic pediatric CMP. On the other hand, during the literature review, we noticed a relatively common etiologic pattern in some forms of complex/multisystem CMP. In other words, certain syndromes such as Danon, Vici, Alström, Barth, and Myhre syndrome share a common pathway of directly or indirectly defective "autophagy" process, which appears to be a possible initiating/triggering factor for CMPs. This conjoint aspect could be important for possible prognostic/therapeutic implications in this category of patients. However, multicentric studies detailed functional and experimental models are needed prior to deriving conclusions.
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Affiliation(s)
- Valentina Lodato
- The European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart-ERN GUARD-Heart, Pediatric Cardiology and Arrhythmia/Syncope Units, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy; (V.L.); (G.P.); (F.C.); (M.S.S.); (F.D.)
| | - Giovanni Parlapiano
- The European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart-ERN GUARD-Heart, Pediatric Cardiology and Arrhythmia/Syncope Units, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy; (V.L.); (G.P.); (F.C.); (M.S.S.); (F.D.)
- Laboratory of Medical Genetics, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - Federica Calì
- The European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart-ERN GUARD-Heart, Pediatric Cardiology and Arrhythmia/Syncope Units, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy; (V.L.); (G.P.); (F.C.); (M.S.S.); (F.D.)
| | - Massimo Stefano Silvetti
- The European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart-ERN GUARD-Heart, Pediatric Cardiology and Arrhythmia/Syncope Units, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy; (V.L.); (G.P.); (F.C.); (M.S.S.); (F.D.)
| | - Rachele Adorisio
- Heart Failure Clinic-Heart Failure, Heart Transplant, Mechanical Circulatory Support Unit, Department of Pediatric Cardiology and Cardiac Surgery, Heart and Lung Transplant, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - Michela Armando
- Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - May El Hachem
- Dermatology and Genodermatosis Units, Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - Antonino Romanzo
- Ophtalmology Unit, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy;
| | - Fabrizio Drago
- The European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart-ERN GUARD-Heart, Pediatric Cardiology and Arrhythmia/Syncope Units, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy; (V.L.); (G.P.); (F.C.); (M.S.S.); (F.D.)
| | - Massimiliano Raponi
- Medical Direction, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy;
| | - Anwar Baban
- The European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart-ERN GUARD-Heart, Pediatric Cardiology and Arrhythmia/Syncope Units, Bambino Gesù Children Hospital and Research Institute, IRCCS, 00165 Rome, Italy; (V.L.); (G.P.); (F.C.); (M.S.S.); (F.D.)
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Baban A, Lodato V, Parlapiano G, Drago F. Genetics in Congenital Heart Diseases: Unraveling the Link Between Cardiac Morphogenesis, Heart Muscle Disease, and Electrical Disorders. Heart Fail Clin 2021; 18:139-153. [PMID: 34776075 DOI: 10.1016/j.hfc.2021.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The genetic background of congenital heart diseases (CHDs) is extremely complex, heterogenous, and still majorly to be determined. CHDs can be sporadic or familial. In this article we discuss in detail the phenotypic spectrum of selected genes including MYH7, GATA4, NKX2-5, TBX5, and TBX20. Our goal is to offer the clinician a general overview of the clinical spectrum of the analyzed topics that are traditionally known as causative for CHDs but we underline in this review the possible progressive functional (cardiomyopathy) and electric aspects (arrhythmias) caused by the genetic background.
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Affiliation(s)
- Anwar Baban
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children Hospital and Research Institute, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
| | - Valentina Lodato
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children Hospital and Research Institute, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - Giovanni Parlapiano
- Laboratory of Medical Genetics, Bambino Gesù Children Hospital and Research Institute, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - Fabrizio Drago
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children Hospital and Research Institute, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
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TAB2 deletions and variants cause a highly recognisable syndrome with mitral valve disease, cardiomyopathy, short stature and hypermobility. Eur J Hum Genet 2021; 29:1669-1676. [PMID: 34456334 DOI: 10.1038/s41431-021-00948-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/27/2021] [Accepted: 08/10/2021] [Indexed: 11/08/2022] Open
Abstract
Deletions that include the gene TAB2 and TAB2 loss-of-function variants have previously been associated with congenital heart defects and cardiomyopathy. However, other features, including short stature, facial dysmorphisms, connective tissue abnormalities and a variable degree of developmental delay, have only been mentioned occasionally in literature and thus far not linked to TAB2. In a large-scale, social media-based chromosome 6 study, we observed a shared phenotype in patients with a 6q25.1 deletion that includes TAB2. To confirm if this phenotype is caused by haploinsufficiency of TAB2 and to delineate a TAB2-related phenotype, we subsequently sequenced TAB2 in patients with matching phenotypes and recruited patients with pathogenic TAB2 variants detected by exome sequencing. This identified 11 patients with a deletion containing TAB2 (size 1.68-14.31 Mb) and 14 patients from six families with novel truncating TAB2 variants. Twenty (80%) patients had cardiac disease, often mitral valve defects and/or cardiomyopathy, 18 (72%) had short stature and 18 (72%) had hypermobility. Twenty patients (80%) had facial features suggestive for Noonan syndrome. No substantial phenotypic differences were noted between patients with deletions and those with intragenic variants. We then compared our patients to 45 patients from the literature. All literature patients had cardiac diseases, but syndromic features were reported infrequently. Our study shows that the phenotype in 6q25.1 deletions is caused by haploinsufficiency of TAB2 and that TAB2 is associated not just with cardiac disease, but also with a distinct phenotype, with features overlapping with Noonan syndrome. We propose the name "TAB2-related syndrome".
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Vahabi N, McDonough CW, Desai AA, Cavallari LH, Duarte JD, Michailidis G. Cox-sMBPLS: An Algorithm for Disease Survival Prediction and Multi-Omics Module Discovery Incorporating Cis-Regulatory Quantitative Effects. Front Genet 2021; 12:701405. [PMID: 34408773 PMCID: PMC8366414 DOI: 10.3389/fgene.2021.701405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/07/2021] [Indexed: 12/03/2022] Open
Abstract
Background The development of high-throughput techniques has enabled profiling a large number of biomolecules across a number of molecular compartments. The challenge then becomes to integrate such multimodal Omics data to gain insights into biological processes and disease onset and progression mechanisms. Further, given the high dimensionality of such data, incorporating prior biological information on interactions between molecular compartments when developing statistical models for data integration is beneficial, especially in settings involving a small number of samples. Results We develop a supervised model for time to event data (e.g., death, biochemical recurrence) that simultaneously accounts for redundant information within Omics profiles and leverages prior biological associations between them through a multi-block PLS framework. The interactions between data from different molecular compartments (e.g., epigenome, transcriptome, methylome, etc.) were captured by using cis-regulatory quantitative effects in the proposed model. The model, coined Cox-sMBPLS, exhibits superior prediction performance and improved feature selection based on both simulation studies and analysis of data from heart failure patients. Conclusion The proposed supervised Cox-sMBPLS model can effectively incorporate prior biological information in the survival prediction system, leading to improved prediction performance and feature selection. It also enables the identification of multi-Omics modules of biomolecules that impact the patients’ survival probability and also provides insights into potential relevant risk factors that merit further investigation.
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Affiliation(s)
- Nasim Vahabi
- Informatics Institute, University of Florida, Gainesville, FL, United States
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, FL, United States
| | - Ankit A Desai
- Department of Medicine, Indiana University, Indianapolis, IN, United States
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, FL, United States
| | - Julio D Duarte
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, FL, United States
| | - George Michailidis
- Informatics Institute, University of Florida, Gainesville, FL, United States
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Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson WD, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PEF, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease. PLoS Genet 2021; 17:e1009679. [PMID: 34324492 PMCID: PMC8354477 DOI: 10.1371/journal.pgen.1009679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/10/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022] Open
Abstract
Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways.
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Affiliation(s)
- Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Anna Wilsdon
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jeroen Breckpot
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Tomas W. Fitzgerald
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anne-Karin Kahlert
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Alejandro Sifrim
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hashim Abdul-Khaliq
- Clinic for Pediatric Cardiology—University Hospital of Saarland, Homburg (Saar), Germany
| | - Mads Bak
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne S. Bassett
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Woodrow D. Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Felix Berger
- Department of Congenital Heart Disease—Pediatric Cardiology, German Heart Center Berlin, Berlin, Germany
| | - Ingo Daehnert
- Department of Pediatric Cardiology and Congenital Heart Disease, Heart Center, University of Leipzig, Leipzig, Germany
| | - Koenraad Devriendt
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sven Dittrich
- Department of Pediatric Cardiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Piers EF Daubeney
- Division of Paediatric Cardiology, Royal Brompton Hospital, London, United Kingdom
| | - Vidu Garg
- The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Center for Cardiovascular Research, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Kirstin Hoff
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Philipp Hofmann
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Gregor Dombrowsky
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Thomas Pickardt
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Ulrike Bauer
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sabine Klaassen
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Pediatric Cardiology, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Hans-Heiner Kramer
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Dianna M. Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Scott Lemaire
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph S. Coselli
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Michael E. Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Aoy Tomita-Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Siddharth K. Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Karl Stamm
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alexandre F. R. Stewart
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Candice K. Silversides
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Brigitte Stiller
- Department of Congenital Heart Disease and Pediatric Cardiology, University Heart Center Freiburg—Bad Krozingen, Freiburg, Germany
| | - Jill A. Rosenfeld
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Inga Vater
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Alex V. Postma
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Almuth Caliebe
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - J. David Brook
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Saint-Justine Research Centre, Université de Montréal, Montreal, Canada
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Bernard Thienpont
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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10
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Liu X, Shang H, Li B, Zhao L, Hua Y, Wu K, Hu M, Fan T. Exploration and validation of hub genes and pathways in the progression of hypoplastic left heart syndrome via weighted gene co-expression network analysis. BMC Cardiovasc Disord 2021; 21:300. [PMID: 34130651 PMCID: PMC8204459 DOI: 10.1186/s12872-021-02108-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/08/2021] [Indexed: 12/18/2022] Open
Abstract
Background Despite significant progress in surgical treatment of hypoplastic left heart syndrome (HLHS), its mortality and morbidity are still high. Little is known about the molecular abnormalities of the syndrome. In this study, we aimed to probe into hub genes and key pathways in the progression of the syndrome. Methods Differentially expressed genes (DEGs) were identified in left ventricle (LV) or right ventricle (RV) tissues between HLHS and controls using the GSE77798 dataset. Then, weighted gene co-expression network analysis (WGCNA) was performed and key modules were constructed for HLHS. Based on the genes in the key modules, protein–protein interaction networks were conducted, and hub genes and key pathways were screened. Finally, the GSE23959 dataset was used to validate hub genes between HLHS and controls. Results We identified 88 and 41 DEGs in LV and RV tissues between HLHS and controls, respectively. DEGs in LV tissues of HLHS were distinctly involved in heart development, apoptotic signaling pathway and ECM receptor interaction. DEGs in RV tissues of HLHS were mainly enriched in BMP signaling pathway, regulation of cell development and regulation of blood pressure. A total of 16 co-expression network were constructed. Among them, black module (r = 0.79 and p value = 2e−04) and pink module (r = 0.84 and p value = 4e−05) had the most significant correlation with HLHS, indicating that the two modules could be the most relevant for HLHS progression. We identified five hub genes in the black module (including Fbn1, Itga8, Itga11, Itgb5 and Thbs2), and five hub genes (including Cblb, Ccl2, Edn1, Itgb3 and Map2k1) in the pink module for HLHS. Their abnormal expression was verified in the GSE23959 dataset. Conclusions Our findings revealed hub genes and key pathways for HLHS through WGCNA, which could play key roles in the molecular mechanism of HLHS.
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Affiliation(s)
- Xuelan Liu
- Department of Children's Heart Center, Henan Provincial People's Hospital, Department of Children's Heart Center of Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China
| | - Honglei Shang
- Department of Radiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Bin Li
- Department of Children's Heart Center, Henan Provincial People's Hospital, Department of Children's Heart Center of Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China
| | - Liyun Zhao
- Department of Children's Heart Center, Henan Provincial People's Hospital, Department of Children's Heart Center of Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China
| | - Ying Hua
- Department of Children's Heart Center, Henan Provincial People's Hospital, Department of Children's Heart Center of Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China
| | - Kaiyuan Wu
- Department of Children's Heart Center, Henan Provincial People's Hospital, Department of Children's Heart Center of Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China
| | - Manman Hu
- Department of Children's Heart Center, Henan Provincial People's Hospital, Department of Children's Heart Center of Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China
| | - Taibing Fan
- Department of Children's Heart Center, Henan Provincial People's Hospital, Department of Children's Heart Center of Fuwai Central China Cardiovascular Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China.
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11
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Yang G, Wang B, Sun D, Wang H, Chen M, Chen H, Zhu B. Genetic association study between TAB2 polymorphisms and noise-induced-hearing-loss in a Han Chinese population. PLoS One 2021; 16:e0251090. [PMID: 33974633 PMCID: PMC8112696 DOI: 10.1371/journal.pone.0251090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/19/2021] [Indexed: 11/18/2022] Open
Abstract
Noise-induced-hearing-loss(NIHL) is a common occupational disease caused by various environmental and biological factors. To investigate the association between TAB2 and the susceptibility of NIHL of people exposed to occupational environments, a genetic association study was performed on selected companies with 588 cases and 537 healthy control subjects. Five selected single nucleotide polymorphisms (SNPs) in TAB2,incoluding rs2744434, rs521845, rs652921, rs7896, rs9485372, were genotyped after a collection of DNA samples. Evident differences in participants between the case group and the control group reveals the result that people with the TAB2 has a high probability of getting NIHL. The results show that rs521845 is deeply associated with the risk of NIHL and is available for the diagnosis in the future.
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Affiliation(s)
- Guangzhi Yang
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
- Department of Prevention and Control for Occupational Disease, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, Jiangsu, China
| | - Boshen Wang
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Dawei Sun
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Huimin Wang
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Mengyao Chen
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hao Chen
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Baoli Zhu
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
- Department of Prevention and Control for Occupational Disease, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, Jiangsu, China
- * E-mail:
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