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Ma Q, Zhang YH, Guo W, Feng K, Huang T, Cai YD. Machine Learning in Identifying Marker Genes for Congenital Heart Diseases of Different Cardiac Cell Types. Life (Basel) 2024; 14:1032. [PMID: 39202774 PMCID: PMC11355424 DOI: 10.3390/life14081032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
Congenital heart disease (CHD) represents a spectrum of inborn heart defects influenced by genetic and environmental factors. This study advances the field by analyzing gene expression profiles in 21,034 cardiac fibroblasts, 73,296 cardiomyocytes, and 35,673 endothelial cells, utilizing single-cell level analysis and machine learning techniques. Six CHD conditions: dilated cardiomyopathy (DCM), donor hearts (used as healthy controls), hypertrophic cardiomyopathy (HCM), heart failure with hypoplastic left heart syndrome (HF_HLHS), Neonatal Hypoplastic Left Heart Syndrome (Neo_HLHS), and Tetralogy of Fallot (TOF), were investigated for each cardiac cell type. Each cell sample was represented by 29,266 gene features. These features were first analyzed by six feature-ranking algorithms, resulting in several feature lists. Then, these lists were fed into incremental feature selection, containing two classification algorithms, to extract essential gene features and classification rules and build efficient classifiers. The identified essential genes can be potential CHD markers in different cardiac cell types. For instance, the LASSO identified key genes specific to various heart cell types in CHD subtypes. FOXO3 was found to be up-regulated in cardiac fibroblasts for both Dilated and hypertrophic cardiomyopathy. In cardiomyocytes, distinct genes such as TMTC1, ART3, ARHGAP24, SHROOM3, and XIST were linked to dilated cardiomyopathy, Neo-Hypoplastic Left Heart Syndrome, hypertrophic cardiomyopathy, HF-Hypoplastic Left Heart Syndrome, and Tetralogy of Fallot, respectively. Endothelial cell analysis further revealed COL25A1, NFIB, and KLF7 as significant genes for dilated cardiomyopathy, hypertrophic cardiomyopathy, and Tetralogy of Fallot. LightGBM, Catboost, MCFS, RF, and XGBoost further delineated key genes for specific CHD subtypes, demonstrating the efficacy of machine learning in identifying CHD-specific genes. Additionally, this study developed quantitative rules for representing the gene expression patterns related to CHDs. This research underscores the potential of machine learning in unraveling the molecular complexities of CHD and establishes a foundation for future mechanism-based studies.
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Affiliation(s)
- Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China;
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China;
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
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Yadav P, Tamilselvan R, Mani H, Singh KK. MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195022. [PMID: 38437914 DOI: 10.1016/j.bbagrm.2024.195022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive. MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3'-untranslated region (3'-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.
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Affiliation(s)
- Priyanka Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Raja Tamilselvan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Harita Mani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Hamadeh IS, Patel JN, Jacobs R, Zeng H, He J, Hu B, Moyo TK, Soni A, Park S, Copelan E, Avalos B, Hamilton A, Steuerwald N, Ghosh N. Genetic Predictors of Ibrutinib-related Cardiovascular Side Effects in Patients with Chronic Lymphocytic Leukemia. Clin Cancer Res 2023; 29:4941-4948. [PMID: 37738027 DOI: 10.1158/1078-0432.ccr-23-0421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/25/2023] [Accepted: 09/20/2023] [Indexed: 09/23/2023]
Abstract
PURPOSE Patients with chronic lymphocytic leukemia (CLL) treated with ibrutinib are at risk of developing cardiovascular side effects (CVSE). The molecular determinants of CVSEs have not been fully elucidated. We interrogated genetic polymorphisms in the Bruton tyrosine kinase (BTK) signaling pathway for their association with ibrutinib-related CVSEs. EXPERIMENTAL DESIGN We conducted a retrospective/prospective observational pharmacogenetic study of 50 patients with newly diagnosed or relapsed CLL who received ibrutinib at a starting daily dose of 420 mg for at least 6 months. CVSEs, primarily atrial fibrillation and hypertension, occurred in 10 patients (20%), of whom 4 discontinued therapy. DNA was isolated from buccal swabs of all 50 patients and genotyped for 40 SNPs in GATA4, SGK1, KCNQ1, KCNA4, NPPA, and SCN5A using a customized next-generation sequencing panel. Univariate and multivariate logistic regression analysis were performed to determine genetic and clinical factors associated with the incidence of ibrutinib-related CVSEs. RESULTS GATA4 rs804280 AA (P = 0.043), KCNQ1 rs163182 GG (P = 0.036), and KCNQ1 rs2237895 AA (P = 0.023) genotypes were univariately associated with ibrutinib-related CVSEs. On the basis of multivariate analysis, a high genetic risk score, defined as the presence of at least two of these genotypes, was associated with 11.5-fold increased odds of CVSEs (P = 0.019; 95% confidence interval, 1.79-119.73). CONCLUSIONS Our findings suggest possible genetic determinants of ibrutinib-related CVSEs in CLL. If replicated in a larger study, pretreatment pharmacogenetic testing for GATA4 and KCNQ1 polymorphisms may be a useful clinical tool for personalizing treatment selection for CLL and/or instituting early risk mitigation strategies.
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Affiliation(s)
- Issam S Hamadeh
- Department of Cancer Pharmacology and Pharmacogenomics, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Jai N Patel
- Department of Cancer Pharmacology and Pharmacogenomics, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Ryan Jacobs
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Hang Zeng
- Department of Cancer Biostatistics, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Jiaxian He
- Department of Cancer Biostatistics, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Bei Hu
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Tamara Kay Moyo
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Amy Soni
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Steven Park
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Ed Copelan
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Belinda Avalos
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Alicia Hamilton
- Molecular Biology and Genomics Core Facility, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Nury Steuerwald
- Molecular Biology and Genomics Core Facility, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
| | - Nilanjan Ghosh
- Department of Hematologic Malignancies and Blood Disorders, Atrium Health Levine Cancer Institute, Charlotte, North Carolina
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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.
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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
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Hong D, Jeong S. 3'UTR Diversity: Expanding Repertoire of RNA Alterations in Human mRNAs. Mol Cells 2023; 46:48-56. [PMID: 36697237 PMCID: PMC9880603 DOI: 10.14348/molcells.2023.0003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/27/2023] Open
Abstract
Genomic information stored in the DNA is transcribed to the mRNA and translated to proteins. The 3' untranslated regions (3'UTRs) of the mRNA serve pivotal roles in posttranscriptional gene expression, regulating mRNA stability, translation, and localization. Similar to DNA mutations producing aberrant proteins, RNA alterations expand the transcriptome landscape and change the cellular proteome. Recent global analyses reveal that many genes express various forms of altered RNAs, including 3'UTR length variants. Alternative polyadenylation and alternative splicing are involved in diversifying 3'UTRs, which could act as a hidden layer of eukaryotic gene expression control. In this review, we summarize the functions and regulations of 3'UTRs and elaborate on the generation and functional consequences of 3'UTR diversity. Given that dynamic 3'UTR length control contributes to phenotypic complexity, dysregulated 3'UTR diversity might be relevant to disease development, including cancers. Thus, 3'UTR diversity in cancer could open exciting new research areas and provide avenues for novel cancer theragnostics.
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Affiliation(s)
- Dawon Hong
- Laboratory of RNA Cell Biology, Department of Bioconvergence Engineering, Dankook University Graduate School, Yongin 16892, Korea
| | - Sunjoo Jeong
- Laboratory of RNA Cell Biology, Department of Bioconvergence Engineering, Dankook University Graduate School, Yongin 16892, Korea
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High throughput mutation screening of cardiac transcription factor GATA4 among Tanzania children with congenital heart diseases. THE NUCLEUS 2023. [DOI: 10.1007/s13237-022-00414-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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7
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Targholi S, Noormohammadi Z, Tafsiri E, Karimipoor M. Evaluation of the Function of a Rare Variant in the 3'-Untranslated Region of the β-Globin Gene. Hemoglobin 2022; 46:312-316. [PMID: 36847660 DOI: 10.1080/03630269.2023.2167660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
β-Thalassemia (β-thal) is an inherited genetic disease that occurs because of the absence or reduction of β-globin chain synthesis. Genetic changes occur in different regions of the β-globin gene, but these mutations are less reported in the 3' untranslated region (3'-UTR). The objective of the present investigation was to evaluate the functional effect of a rare variant in the 3'-UTR of the β-globin gene. A variant at the first nucleotide of the 3'-UTR of the β-globin gene (HBB: c.*1G > A) was identified by DNA sequencing in an individual with low hematological indices and a normal hemoglobin (Hb) electrophoresis pattern. To evaluate the functional effect of this variant, the normal and mutated 3'-UTR of the β-globin gene was synthesized separately and sub cloned in the psiCHEK2 vector. Next, using the calcium phosphate method, the psiCHEK2 vectors containing normal and mutated 3'-UTR were transfected separately into the HEK293T cell line. Finally, the transfected cell line was analyzed by dual luciferase assay. The ratio of Renilla to firefly for the mutant sample was 1.26 ± 0.06, while for normal samples it was 1.12 ± 0.04. The results of the luciferase assay showed that there was no significant difference in the functional effect between the mutant and wild type construct. Therefore, it was concluded that this variant might not reduce the expression of the β-globin gene. Future studies by globin chain synthesis or to evaluate the expression of the gene in erythroid cells, might be necessary to understand the regulatory function of this mutation.
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Affiliation(s)
- Sogol Targholi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Noormohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Elham Tafsiri
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Zhang Z, Liu C, Hao W, Yin W, Ai S, Zhao Y, Duan Z. Novel Single Nucleotide Polymorphisms and Haplotype of MYF5 Gene Are Associated with Body Measurements and Ultrasound Traits in Grassland Short-Tailed Sheep. Genes (Basel) 2022; 13:genes13030483. [PMID: 35328037 PMCID: PMC8949509 DOI: 10.3390/genes13030483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Myogenic factor 5 plays active roles in the regulation of myogenesis. The aim of this study is to expose the genetic variants of the MYF5 and its association with growth performance and ultrasound traits in grassland short-tailed sheep (GSTS) in China. The combination technique of sequencing and SNaPshot revealed seven SNPs in ovine MYF5 from 533 adult individuals (male 103 and female 430), four of which are novel ones located at g.6838G > A, g.6989 G > T, g.7117 C > A in the promoter region and g.9471 T > G in the second intron, respectively. Genetic diversity indexes showed the seven SNPs in low or intermediate level, but each of them conformed HWE (p > 0.05) in genotypic frequencies. Association analysis indicated that g.6838G > A, g.7117 C > A, g.8371 T > C, g.9471 T > G, and g.10044 C > T had significant effects on growth performance and ultrasound traits. The diplotypes of H1H3 and H2H3 had higher body weight and greater body size, and haplotype H3 had better performance on meat production than the others. In addition, the dual-luciferase reporter assay showed that there are two active regions in the MYF5 promoter located at −1799~−1197 bp and −514~−241 bp, respectively, but g.6838G > A and g.7117 C > A were out of the region, suggesting these two SNPs influence the phenotype by other pathway. The results suggest that the MYF5 gene might be applied as a promising candidate of functional genetic marker in GSTS breeding.
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Affiliation(s)
- Zhichao Zhang
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Liu
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Wenjing Hao
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Weiwen Yin
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Sitong Ai
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Yanfang Zhao
- Animal Disease Prevention and Control Center, Ewenki Autonomous Banner, Hulunbuir 021000, China;
| | - Ziyuan Duan
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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Abbasi S, Mohsen-Pour N, Naderi N, Rahimi S, Maleki M, Kalayinia S. In silico analysis of GATA4 variants demonstrates main contribution to congenital heart disease. J Cardiovasc Thorac Res 2021; 13:336-354. [PMID: 35047139 PMCID: PMC8749364 DOI: 10.34172/jcvtr.2021.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/05/2021] [Accepted: 09/24/2021] [Indexed: 12/05/2022] Open
Abstract
Introduction: Congenital heart disease (CHD) is the most common congenital abnormality and the main cause of infant mortality worldwide. Some of the mutations that occur in the GATA4 gene region may result in different types of CHD. Here, we report our in silico analysis of gene variants to determine the effects of the GATA4 gene on the development of CHD.
Methods: Online 1000 Genomes Project, ExAC, gnomAD, GO-ESP, TOPMed, Iranome, GME, ClinVar, and HGMD databases were drawn upon to collect information on all the reported GATA4 variations.The functional importance of the genetic variants was assessed by using SIFT, MutationTaster, CADD,PolyPhen-2, PROVEAN, and GERP prediction tools. Thereafter, network analysis of the GATA4protein via STRING, normal/mutant protein structure prediction via HOPE and I-TASSER, and phylogenetic assessment of the GATA4 sequence alignment via ClustalW were performed.
Results: The most frequent variant was c.874T>C (45.58%), which was reported in Germany.Ventricular septal defect was the most frequent type of CHD. Out of all the reported variants of GATA4,38 variants were pathogenic. A high level of pathogenicity was shown for p.Gly221Arg (CADD score=31), which was further analyzed.
Conclusion: The GATA4 gene plays a significant role in CHD; we, therefore, suggest that it be accorded priority in CHD genetic screening.
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Affiliation(s)
- Shiva Abbasi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Mohsen-Pour
- Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Niloofar Naderi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Shahin Rahimi
- Department of Cardiology, Rajaie Cardiovascular Medical and Research Centre, 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
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
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Khatami M, Ghorbani S, Adriani MR, Bahaloo S, Naeini MA, Heidari MM, Hadadzadeh M. Novel Point Mutations in 3'-Untranslated Region of GATA4 Gene Are Associated with Sporadic Non-syndromic Atrial and Ventricular Septal Defects. Curr Med Sci 2021; 42:129-143. [PMID: 34652630 DOI: 10.1007/s11596-021-2428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/14/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Transcription factor GATA4 has significant roles in embryonic heart development. Mutations of GATA4 appear to be responsible for a wide variety of congenital heart defects (CHD). Despite the high prevalence of GATA4 mutations in CHD phenotypes, extensive studies have not been performed. The 3'-untranslated region (3'-UTR) of the GATA4 gene comprises regulatory motifs and microRNA binding sites that are critical for the appropriate gene expression, nuclear transportation, and regulation of translation, and stability of mRNA. This study aimed to evaluate the association between mutations in the 3'-UTR of the GATA4 gene and CHD risk among Iranian patients. METHODS We analyzed the coding region of exon 6 and the whole 3'-UTR of GATA4 in DNA isolated from 175 blood samples of CHD patients and 115 unrelated healthy individuals. The functional importance of the observed GATA4 mutations was evaluated using a variety of bioinformatics algorithms for assessment of nonsynonymous mutations and those observed in miRNA binding sites of 3'-UTR. RESULTS Twenty-one point mutations including one missense mutation (c.511A>G: p.Ser377Gly) in exon 6 and 20 nucleotide variations in 3'-UTR of GATA4 gene were identified in 65 of the 175 CHD patients. In our patients, we identified 12 novel sequence alterations and 8 single nucleotide polymorphisms in the 3'-UTR of GATA4. Most of them had statistically significant differences between CHD patients and controls. CONCLUSION Our results suggest that 3'-UTR variations of the GATA4 gene probably change microRNA binding sites and present an additional molecular risk factor for the susceptibility of CHD.
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Affiliation(s)
- Mehri Khatami
- Department of Biology, Faculty of Science, Yazd University, Yazd, 8915818411, Iran.
| | - Sajedeh Ghorbani
- Department of Biology, Faculty of Science, Yazd University, Yazd, 8915818411, Iran
| | | | - Sahar Bahaloo
- Department of Biology, Faculty of Science, Yazd University, Yazd, 8915818411, Iran
| | - Mehri Azami Naeini
- Department of Biology, Faculty of Science, Yazd University, Yazd, 8915818411, Iran
| | | | - Mehdi Hadadzadeh
- Department of Cardiac Surgery, Afshar Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, 8915887856, Iran
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11
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Wright CF, Quaife NM, Ramos-Hernández L, Danecek P, Ferla MP, Samocha KE, Kaplanis J, Gardner EJ, Eberhardt RY, Chao KR, Karczewski KJ, Morales J, Gallone G, Balasubramanian M, Banka S, Gompertz L, Kerr B, Kirby A, Lynch SA, Morton JEV, Pinz H, Sansbury FH, Stewart H, Zuccarelli BD, Cook SA, Taylor JC, Juusola J, Retterer K, Firth HV, Hurles ME, Lara-Pezzi E, Barton PJR, Whiffin N. Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms. Am J Hum Genet 2021; 108:1083-1094. [PMID: 34022131 PMCID: PMC8206381 DOI: 10.1016/j.ajhg.2021.04.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023] Open
Abstract
Clinical genetic testing of protein-coding regions identifies a likely causative variant in only around half of developmental disorder (DD) cases. The contribution of regulatory variation in non-coding regions to rare disease, including DD, remains very poorly understood. We screened 9,858 probands from the Deciphering Developmental Disorders (DDD) study for de novo mutations in the 5' untranslated regions (5' UTRs) of genes within which variants have previously been shown to cause DD through a dominant haploinsufficient mechanism. We identified four single-nucleotide variants and two copy-number variants upstream of MEF2C in a total of ten individual probands. We developed multiple bespoke and orthogonal experimental approaches to demonstrate that these variants cause DD through three distinct loss-of-function mechanisms, disrupting transcription, translation, and/or protein function. These non-coding region variants represent 23% of likely diagnoses identified in MEF2C in the DDD cohort, but these would all be missed in standard clinical genetics approaches. Nonetheless, these variants are readily detectable in exome sequence data, with 30.7% of 5' UTR bases across all genes well covered in the DDD dataset. Our analyses show that non-coding variants upstream of genes within which coding variants are known to cause DD are an important cause of severe disease and demonstrate that analyzing 5' UTRs can increase diagnostic yield. We also show how non-coding variants can help inform both the disease-causing mechanism underlying protein-coding variants and dosage tolerance of the gene.
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Affiliation(s)
- Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter EX2 5DW, UK
| | - Nicholas M Quaife
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Laura Ramos-Hernández
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Matteo P Ferla
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Katherine R Chao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield S10 2TH, UK; Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield S10 2TH, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Lianne Gompertz
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Bronwyn Kerr
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Amelia Kirby
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Sally A Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin D01 XD99, Ireland
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Hailey Pinz
- Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Francis H Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4AY, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Britton D Zuccarelli
- Department of Neurology, University of Kansas School of Medicine-Salina Campus, Salina, KS 67401, USA
| | - Stuart A Cook
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; CIBER de enfermedades CardioVasculares (CIBERCV), 28029 Madrid, Spain
| | - Paul J R Barton
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Nicola Whiffin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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12
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Noori NM, shahraki Z, Karimi F, Miri-Moghaddam E. Rs4841587 in GATA4 and rs6999593 in DNMT1 gene associated with congenital heart diseases in the southeast of Iran. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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Kader F, Ghai M, Olaniran AO. Characterization of DNA methylation-based markers for human body fluid identification in forensics: a critical review. Int J Legal Med 2019; 134:1-20. [PMID: 31713682 DOI: 10.1007/s00414-019-02181-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
Abstract
Body fluid identification in crime scene investigations aids in reconstruction of crime scenes. Several studies have identified and reported differentially methylated sites (DMSs) and regions (DMRs) which differ between forensically relevant tissues (tDMRs) and body fluids. Diverse factors affect methylation patterns such as the environment, diets, lifestyle, disease, ethnicity, genetic variation, amongst others. Thus, it is important to analyse the stability of markers employed for forensic identification. Furthermore, even though epigenetic modifications are described as stable and heritable, epigenetic inheritance of potential markers for body fluid identification needs to be assessed in the long term. Here, we discuss the current status of reported DNA methylation-based markers and their verification studies. Such thorough investigation is crucial to develop a stable panel of DNA methylation-based markers for accurate body fluid identification.
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Affiliation(s)
- Farzeen Kader
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa.
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
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14
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Yee J, Kim W, Chang BC, Chung JE, Lee KE, Gwak HS. Genetic variations in the transcription factors GATA4 and GATA6 and bleeding complications in patients receiving warfarin therapy. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:1717-1727. [PMID: 31190750 PMCID: PMC6529806 DOI: 10.2147/dddt.s198018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/19/2019] [Indexed: 12/17/2022]
Abstract
Purpose: GATA4 and GATA6 are known to have potential roles in vascular regulation by affecting vascular smooth muscle cell differentiation and atrial natriuretic peptide levels. The aim of this retrospective study was to investigate the associations between GATA4 and GATA6 polymorphisms and bleeding complication risk at a therapeutic international normalized ratio (INR) in patients with mechanical heart valves. Patients and methods: Study patients were included from the Ewha-Severance Treatment (EAST) Group of Warfarin. It consisted of 229 patients who received warfarin therapy after undergoing mechanical heart valve replacement and maintained a stable INR (INR of 2.0–3.0 for at least three consecutive times). Twenty single-nucleotide polymorphisms including VKORC1, CYP2C9, GATA4, and GATA6 were analyzed. Multivariate logistic regression analysis was employed to investigate the independent risk factors for bleeding complications. To evaluate the potential clinical value of genotyping for preventing bleeding complications in patients with high-risk genotype, the number needed to genotype (NNG) was also calculated. Results: One hundred forty-two patients were included in this study, 21 of whom had bleeding complications. After adjusting covariates, TT genotype carriers of rs13273672 in GATA4 and CC genotype carriers of rs10454095 in GATA6 showed 5.0- (95% CI, 1.6–15.7) and 3.1-fold (95% CI, 1.1–8.7) higher bleeding complications than carriers of C allele and T allele, respectively. NNG for preventing one patient from experiencing bleeding complications in patients with TT genotype of rs13273672 and CC genotype of rs10454095 was 22.2 and 17.5, respectively. Patients with both TT genotype in rs13273672 and CC genotype in rs10454095 showed 8.7-fold (95% CI, 1.7–46.1) higher bleeding complications than those with other genotypes. NNG in patients having both TT genotype in rs13273672 and CC genotype in rs10454095 was calculated to be 40.0. Conclusions: This study showed that GATA4 and GATA6 gene polymorphisms could affect bleeding complications during warfarin treatment in patients with mechanical heart valves.
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Affiliation(s)
- Jeong Yee
- College of Pharmacy & Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Woorim Kim
- College of Pharmacy, Chungbuk National University, Cheongju-si 28160, Korea
| | - Byung Chul Chang
- Department of Thoracic and Cardiovascular Surgery, Bundang CHA Medical Center, CHA University, Seongnam, Gyeonggi-do, Korea.,Department of Thoracic & Cardiovascular Surgery, Yonsei University Medical Center, Seoul 03722, Korea
| | - Jee Eun Chung
- College of Pharmacy, Hanyang University, Ansan 15588, Korea
| | - Kyung Eun Lee
- College of Pharmacy, Chungbuk National University, Cheongju-si 28160, Korea
| | - Hye Sun Gwak
- College of Pharmacy & Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
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15
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Riachi M, Bas F, Darendeliler F, Hussain K. A novel 3' untranslated region mutation in the SLC29A3 gene associated with pigmentary hypertrichosis and non-autoimmune insulin-dependent diabetes mellitus syndrome. Pediatr Diabetes 2019; 20:474-481. [PMID: 30821020 DOI: 10.1111/pedi.12839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 01/08/2019] [Accepted: 02/08/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Pigmentary hypertrichosis and non-autoimmune insulin-dependent diabetes mellitus (PHID) is one of the rare H syndrome diseases mainly characterized by hyperpigmentation, hypertrichosis, sensorineural hearing loss, cardiac complications, developmental delay, and diabetes mellitus (DM). Mutations in the coding regions of the SLC29A3 gene that encodes for an equilibrative nucleoside transporter (ENT3) have been reported to cause the phenotypic spectrum of the H syndrome. Disease-causing mutations in the untranslated regions (UTRs) of the SLC29A3 gene have not been previously described in the literature. The aim of the study is to describe and assess the pathogenicity of a novel 3'UTR mutation in the SLC29A3 gene associated with the PHID phenotype in two Turkish patients. METHODS The mutation was identified by a targeted gene approach. To understand the pathogenicity of this 3'UTR mutation, RNA and protein expression studies were performed by using the quantitative real-time polymerase chain reaction method and western blotting, respectively, using fibroblasts cultured from the patients' skin biopsies. RESULTS SLC29A3 and ENT3 expression levels were both decreased in the patients compared to controls matched for passage numbers, RNA, and protein extraction methods. CONCLUSIONS A novel 3'UTR mutation in the SLC29A3 gene is associated with the PHID syndrome, highlighting a potentially new pathological mechanism for this disease. The involvement of the 3'UTR has not been previously established in any of the H syndrome disease cluster or in any complex syndrome of DM.
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Affiliation(s)
- Melissa Riachi
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Firdevs Bas
- Department of Pediatrics, Pediatric Endocrinology Unit, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Feyza Darendeliler
- Department of Pediatrics, Pediatric Endocrinology Unit, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Khalid Hussain
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK.,Department of Pediatrics, Division of Endocrinology, Sidra Medicine, Doha, Qatar
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16
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Hosseindokht M, Boroumand M, Salehi R, Mandegary A, Hajhosseini Talasaz A, Pourgholi L, Zare H, Ziaee S, Sharifi M. Association between four microRNA binding site-related polymorphisms and the risk of warfarin-induced bleeding complications. EXCLI JOURNAL 2019; 18:287-299. [PMID: 31338002 PMCID: PMC6635724 DOI: 10.17179/excli2019-1352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/02/2019] [Indexed: 12/18/2022]
Abstract
Bleeding is the most serious complication of warfarin anticoagulation therapy and is known to occur even at patients with therapeutic international normalized ratio (INR) range. Recently, it has been shown that microRNAs play a significant role in pharmacogenetics by regulating genes that are critical for drug function. Interaction between microRNAs and these target genes could be affected by single-nucleotide polymorphisms (SNPs) located in microRNA-binding sites. This study focused on 3′-untranslated region (3′-UTR) SNPs of the genes involved in the warfarin action and the occurrence of bleeding complications in an Iranian population receiving warfarin. A total of 526 patients under warfarin anticoagulation therapy with responding to the therapeutic dose and maintenance of the INR in the range of 2.0-3.5 in three consecutive blood tests were included in the study. Four selected 3'-UTR SNPs (rs12458, rs7294, rs1868774 and rs34669593 located in GATA4, VKORC1, CALU and GGCX genes, respectively) with the potential to disrupt/eliminate or enhance/create microRNA-binding site were genotyped using a simple PCR-based restriction fragment length polymorphism (PCR-RFLP) method. Patients with the rs12458 AT or TT genotypes of the GATA4 gene had a lower risk of bleeding compared to patients with the AA genotype (adjusted OR: 0.478, 95% CI: 0.285-0.802, P= 0.005, OR: 0.416, 95% CI: 0.192-0.902, P= 0.026, respectively). 3'-UTR polymorphisms in other genes were not significantly associated with the risk of bleeding complications. In conclusion, the SNP rs12458A>T in the 3′UTR region of GATA4 is associated with the incidence of warfarin-related bleeding at target range of INR, likely by altering microRNA binding and warfarin metabolism. Further genetics association studies are needed to validate these findings before they can be implemented in clinical settings.
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Affiliation(s)
- Maryam Hosseindokht
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammadali Boroumand
- Department of Pathology and Laboratory Medicine, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Mandegary
- Department of Pharmacology and Toxicology, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran; Gastroenterology and Hepatology Research Center, Afzalipour's Hospital, Imam Highway, Kerman, Iran
| | - Azita Hajhosseini Talasaz
- Department of Cardiac Research, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Clinical Pharmacy, School of Pharmacy, Tehran University of Medical Sciences
| | - Leyla Pourgholi
- Department of Pathology and Laboratory Medicine, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamed Zare
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Shayan Ziaee
- Department of Pathology and Laboratory Medicine, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Sharifi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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17
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Jay K, Mitra A, Harding T, Matthes D, Van Ness B. Identification of a de novo FOXP1 mutation and incidental discovery of inherited genetic variants contributing to a case of autism spectrum disorder and epilepsy. Mol Genet Genomic Med 2019; 7:e00751. [PMID: 31111659 PMCID: PMC6625142 DOI: 10.1002/mgg3.751] [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: 01/27/2019] [Revised: 04/08/2019] [Accepted: 04/22/2019] [Indexed: 12/15/2022] Open
Abstract
Background Autism spectrum disorder is commonly co‐diagnosed intellectual disability, language disorder, anxiety, and epilepsy, however, symptom management is difficult due to the complex genetic nature of ASD. Methods We present a next‐generation sequencing‐based case study with both de novo and inherited genetic variants and highlight the impact of structural variants on post‐translational regulation of protein expression. Since management of symptoms has classically been through pharmaceutical therapies, a pharmacogenomics screen was also utilized to determine possible drug/gene interactions. Results A de novo variant was identified within the FOXP1 3′ untranslated regulatory region using exome sequencing. Additionally, inherited variants that likely contribute to the current and potential future traits were identified within the COMT, SLC6A4, CYP2C19, and CYP2D6 genes. Conclusion This study aims to elucidate how a collection of variant genotypes could potentially impact neural development resulting in a unique phenotype including ASD and epilepsy. Each gene's contribution to neural development is assessed, and the interplay of these genotypes is discussed. The results highlight the utility of exome sequencing in conjunction with pharmacogenomics screening when evaluating possible causes of and therapeutic treatments for ASD‐related symptoms.
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Affiliation(s)
- Kristy Jay
- College of Biological Sciences, Department of Genetics, Cell Biology, and Development, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Amit Mitra
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, Alabama
| | - Taylor Harding
- College of Biological Sciences, Department of Genetics, Cell Biology, and Development, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - David Matthes
- College of Biological Sciences, Department of Biology, Teaching, and Learning, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Brian Van Ness
- College of Biological Sciences, Department of Genetics, Cell Biology, and Development, University of Minnesota-Twin Cities, Minneapolis, Minnesota
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18
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Implication of GATA4 synonymous variants in congenital heart disease: A comprehensive in-silico approach. Mutat Res 2018; 813:31-38. [PMID: 30590232 DOI: 10.1016/j.mrfmmm.2018.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/17/2018] [Accepted: 12/14/2018] [Indexed: 11/22/2022]
Abstract
Synonymous variations, previously considered as neutral, are recently shown to have a significant impact on mRNA structure and stability thereby affecting protein expression and function. Their role in disease pathogenesis is also emerging. GATA4 is an important transcription factor involved in cardiac development and a well-known candidate gene associated with congenital heart disease (CHD). In the present study, we sought to conduct molecular screening of GATA4 gene in 285 sporadic and non-syndromic CHD cases. We identified four synonymous (c.27C>A, c.822C>T, c.1233G>A and c.1263C>T) and two intronic variants (g.83217T>G & g.85012T>A) in GATA4. Extensive computational analysis using widely acceptable tools i.e., Mfold, Human Splicing Finder (HSF) and Codon Usage bias was performed with a view to understand their putative downstream effects on GATA4 function. Mfold, a mRNA structure prediction tool showed the alterations of the mRNA structure and stability due to synonymous variants. Similarly, HSF also confidently predicted effect on the cis-acting regulatory elements of splicing due to four synonymous and one donor site intronic variants. Additionally, a significant change in 'Relative Synonymous Codon usage (RSCU) frequencies' and 'log ratio of codon usage frequencies' of variant codon was also noted that might affect the rate of translation. This study establishes that the synonymous variants are possibly associated with disease phenotype in CHD patients. Comprehensive computational analysis, using well-established web based tools, is suggestive of their potential downstream molecular effects on the structure, stability and expression of GATA4 protein.
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19
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Doñate Puertas R, Jalabert A, Meugnier E, Euthine V, Chevalier P, Rome S. Analysis of the microRNA signature in left atrium from patients with valvular heart disease reveals their implications in atrial fibrillation. PLoS One 2018; 13:e0196666. [PMID: 29723239 PMCID: PMC5933750 DOI: 10.1371/journal.pone.0196666] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Among the potential factors which may contribute to the development and perpetuation of atrial fibrillation, dysregulation of miRNAs has been suggested. Thus in this study, we have quantified the basal expressions of 662 mature human miRNAs in left atrium (LA) from patients undergoing cardiac surgery for valve repair, suffering or not from atrial fibrillation (AF) by using TaqMan® Low Density arrays (v2.0). RESULTS Among the 299 miRNAs expressed in all patients, 42 miRNAs had altered basal expressions in patients with AF. Binding-site predictions with Targetscan (conserved sites among species) indicated that the up- and down-regulated miRNAs controlled respectively 3,310 and 5,868 genes. To identify the most relevant cellular functions under the control of the altered miRNAs, we focused on the 100 most targeted genes of each list and identified 5 functional protein-protein networks among these genes. Up-regulated networks were involved in synchronisation of circadian rythmicity and in the control of the AKT/PKC signaling pathway (i.e., proliferation/adhesion). Down-regulated networks were the IGF-1 pathway and TGF-beta signaling pathway and a network involved in RNA-mediated gene silencing, suggesting for the first time that alteration of miRNAs in AF would also perturbate the whole miRNA machinery. Then we crossed the list of miRNA predicted genes, and the list of mRNAs altered in similar patients suffering from AF and we found that respectively 44.5% and 55% of the up- and down-regulated mRNA are predicted to be conserved targets of the altered miRNAs (at least one binding site in 3'-UTR). As they were involved in the same biological processes mentioned above, these data demonstrated that a great part of the transcriptional defects previously published in LA from AF patients are likely due to defects at the post-transcriptional level and involved the miRNAs. CONCLUSIONS Our stringent analysis permitted us to identify highly targeted protein-protein networks under the control of miRNAs in LA and, among them, to highlight those specifically affected in AF patients with altered miRNA signature. Further studies are now required to determine whether alterations of miRNA levels in AF pathology are causal or represent an adaptation to prevent cardiac electrical and structural remodeling.
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Affiliation(s)
- Rosa Doñate Puertas
- Institut NeuroMyoGene (INMG), UMR CNRS 5310-INSERM U1217 / University of Lyon, Lyon, France
| | - Audrey Jalabert
- CarMeN Laboratory (UMR INSERM 1060-INRA 1397, INSA), Lyon-Sud Faculty of Medicine, University of Lyon, Pierre-Bénite, France
| | - Emmanuelle Meugnier
- CarMeN Laboratory (UMR INSERM 1060-INRA 1397, INSA), Lyon-Sud Faculty of Medicine, University of Lyon, Pierre-Bénite, France
| | - Vanessa Euthine
- CarMeN Laboratory (UMR INSERM 1060-INRA 1397, INSA), Lyon-Sud Faculty of Medicine, University of Lyon, Pierre-Bénite, France
| | - Philippe Chevalier
- Institut NeuroMyoGene (INMG), UMR CNRS 5310-INSERM U1217 / University of Lyon, Lyon, France
- Rhythmology Unit, Louis Pradel Cardiology Hospital, Hospices Civils de Lyon, Bron, France
- * E-mail: (SR); (PC)
| | - Sophie Rome
- CarMeN Laboratory (UMR INSERM 1060-INRA 1397, INSA), Lyon-Sud Faculty of Medicine, University of Lyon, Pierre-Bénite, France
- * E-mail: (SR); (PC)
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20
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Bose D, D V, Shetty M, J K, Kutty AVM. Identification of intronic-splice site mutations in GATA4 gene in Indian patients with congenital heart disease. Mutat Res 2017; 803-805:26-34. [PMID: 28843068 DOI: 10.1016/j.mrfmmm.2017.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/01/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
Abstract
Congenital Heart Disease (CHD) is the most common birth defect among congenital anomalies that arise before birth. GATA4 transcription factor plays an important role in foetal heart development. Mutational analysis of GATA4 gene in CHD patients revealed five known heterozygous mutations (p.T355S, p.S377G, p.V380M, p.P394T and p.D425N) identified in exons 5 and 6 regions and fifteen intronic variants in the non-coding regions (g.76885T>C/Y,g.76937G>S, g.78343G>R, g.83073T>Y, g.83271C>A/M, g.83318G>K, g.83415G>R, g.83502A>C/M, g.84991G>R, g.85294C>Y, g.85342C>T/Y, g.86268A>R, g.87409G>A/R, g.87725T>Y, g.87813A>T/W). In silico analysis of these intronic variants identified two potential branch point mutations (g.83271C>A/M, g.86268A>R) and predicted effects of these on intronic splice sites as enhancer and silencer motifs. This study attempts to correlate the pattern of intronic variants of GATA4 gene which might provide new insights to unravel the possible molecular etiology of CHD.
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Affiliation(s)
- Divya Bose
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India
| | - Vaigundan D
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India
| | - Mitesh Shetty
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India
| | - Krishnappa J
- Department of Pediatrics, Sri Devaraj Urs Medical College, R. L. Jalappa Hospital and Research Centre, Tamaka, Kolar, Karnataka, India
| | - A V M Kutty
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India.
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21
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Zhang Y, Ai F, Zheng J, Peng B. Associations of GATA4 genetic mutations with the risk of congenital heart disease: A meta-analysis. Medicine (Baltimore) 2017; 96:e6857. [PMID: 28471988 PMCID: PMC5419936 DOI: 10.1097/md.0000000000006857] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND GATA4 gene is a cardiac transcriptional factor playing important role in cardiac formation and development. Three GATA4 gene mutations, 99 G>T, 487 C>T, and 354 A>C, have been reported in congenital heart disease (CHD). Therefore, a meta-analysis was performed to explore the associations between 99 G>T, 487 C>T, or 354 A>C mutations and the risk of CHD. METHODS We searched the relevant studies in electronic databases, including ISI Science Citation Index, Embase, PubMed, CNKI, and Wan fang, from January 2006 to March 2016. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to estimate the associations between 99 G>T, 487 C>T, or 354 A>C mutations and the risk of CHD. RESULTS A total of 11 studies including 2878 CHD cases and 3339 controls were evaluated. There was no significant association between GATA4 99 G>T (OR = 1.22, 95% CI = 0.74-2.01, P = .43) or 487 C>T (OR = 1.16, 95% CI = 0.48-2.78, P = .74) mutations and the risk of CHD, whereas GATA4 354 A>C (OR = 1.49, 95% CI = 1.15-1.93, P = .003) mutation was significantly associated with CHD risk. Subgroup analysis was further performed for GATA4 99 G>T, 487 C>T, and 354 A>C mutations based on sample size and ethnicity, and no significant association between GATA4 99 G>T or 487 C>T mutations and the risk of CHD was found in all subgroups, whereas GATA4 354 A>C mutation was significantly associated with CHD risk in large-sample-size and Asian subgroups. However, subgroup analysis by types of CHD indicated that there was no significant association between GATA4 354 A>C mutation and the risk of ventricular septal defects. CONCLUSIONS Our findings suggested that GATA4 99 G>T and 487 C>T mutations may not be related to the incidence of CHD. However, GATA4 354 A>C mutation was significantly associated with CHD risk.
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22
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Su W, Zhu P, Wang R, Wu Q, Wang M, Zhang X, Mei L, Tang J, Kumar M, Wang X, Su L, Dong N. Congenital heart diseases and their association with the variant distribution features on susceptibility genes. Clin Genet 2016; 91:349-354. [PMID: 27426723 DOI: 10.1111/cge.12835] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 01/07/2023]
Abstract
Congenital heart disease (CHD), one of the causes of childhood morbidity and mortality, is mainly triggered by a combination of environmental and genetic factors. Several susceptible genes, such as NKX2-5, GATA4 and TBX5, have been reported as closely related to heart and vessel development. CHD subtypes are classified into diverse clinical phenotypes, such as atrial septal defects (ASD), ventricular septal defects (VSD), tetralogy of Fallot (TOF), and Holt-Oram syndrome (HOS). Here, we summarize the associations of the genetic variants in these three genes with CHD subtypes. CHD-associated variants of NKX2-5 locate mainly in the tinman domain and the homeodomain. Mutations in the homeodomain are correlated with ASD and atrioventricular (AV) block subtypes. VSD-associated variants of GATA4 are mainly at its terminal ends. Variants of TBX5 gene are primarily in exons 3, 4, 5 and 7 and highly associated with HOS subtype. Hence, the variant distribution of NKX2-5, GATA4 and TBX5 are tightly associated with particular CHD subtypes. Further structure-modelling analysis revealed that these mutated amino acid residuals maintain their DNA-binding ability and structural stability. Therefore structural features of these genes may be used to predict the high risk of CHD subtypes in infants.
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Affiliation(s)
- W Su
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - P Zhu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - R Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Q Wu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - M Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - X Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - L Mei
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - J Tang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - M Kumar
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - X Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - L Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - N Dong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Los polimorfismos de nucleótido único y los haplotipos de la región 3’UTR del gen GATA4 contribuyen al riesgo genético de cardiopatía congénita. Rev Esp Cardiol 2016. [DOI: 10.1016/j.recesp.2015.12.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Zhang L, Ma X, Xuan J, Wang H, Yuan Z, Wu M, Liu R, Zhu C, Wei C, Zhao F, Du L. Identification of MEF2B and TRHDE Gene Polymorphisms Related to Growth Traits in a New Ujumqin Sheep Population. PLoS One 2016; 11:e0159504. [PMID: 27472808 PMCID: PMC4966928 DOI: 10.1371/journal.pone.0159504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/05/2016] [Indexed: 11/21/2022] Open
Abstract
2 SNPs were discovered in our previous genome-wide association study (GWAS): s58995.1 (rs420767326 A>G) in MEF2B gene and OAR3_115712045.1 (rs401775061 A>C) in TRHDE gene, which were significantly associated with post-weaning gain in sheep. Herein, we performed a replication experiment to investigate single nucleotide polymorphisms (SNPs) within the MEF2B and TRHDE gene exons, the 5′untranslated regions (within 1000bp), the 3′ untranslated regions (within 1000bp) and their associations with Ujumqin sheep growth traits in 4-month age and 6-month age, respectively. Finally,3 SNPs were selected to be investigated including 1 SNP in 3′untranslated regions in MEF2B gene (rs417014745 A>G) and 2 SNPs in TRHDE gene (rs426980328 T>C and rs430810656 G>A).The χ2 test showed all the 3 variations were in Hardy–Weinberg equilibrium (P>0.05) status. Association analysis suggested that rs426980328 T>C was significantly associated with body weight and chest girth in 4-month age (P<0.05). rs430810656 G>A exhibited extremely significant association with body weight and chest girth in 4-month age (P<0.01). rs417014745 A>G was extremely significantly associated with body weight and chest girth in 4-month age and chest girth in 6-month age (P<0.01), and it was also significantly associated with body weight in 6-month age (P<0.05). Combined effect analysis indicated significant associations between the combinations of rs426980328-rs417014745, rs430810656-rs417014745 and several growth traits (P<0.05). These results suggested MEF2B and TRHDE genes affected growth traits in Ujumqin sheep and the combination effect of the two genes also played a significant effective role. These SNPs might have potential value as genetic markers for growth traits and it could be used in Ujumqin sheep breeding in future. Further studies are necessary to confirm our findings.
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Affiliation(s)
- Li Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaomeng Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junli Xuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zehu Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingming Wu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruizao Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Caiye Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lixin Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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25
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A gain-of-function ACTC1 3'UTR mutation that introduces a miR-139-5p target site may be associated with a dominant familial atrial septal defect. Sci Rep 2016; 6:25404. [PMID: 27139165 PMCID: PMC4853704 DOI: 10.1038/srep25404] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/18/2016] [Indexed: 12/29/2022] Open
Abstract
The ostium secundum atrial septal defect (ASDII) is the most common type of congenital heart disease and is characterized by a left to right shunting of oxygenated blood caused by incomplete closure of the septum secundum. We identified a familial form of isolated ASDII that affects four individuals in a family of five and shows autosomal dominant inheritance. By whole genome sequencing, we discovered a new mutation (c.*1784T > C) in the 3′-untranslated region (3′UTR) of ACTC1, which encodes the predominant actin in the embryonic heart. Further analysis demonstrated that the c.*1784T > C mutation results in a new target site for miRNA-139-5p, a microRNA that is involved in cell migration, invasion, and proliferation. Functional analysis demonstrated that the c.*1784T > C mutation specifically downregulates gene expression in a luciferase assay. Additionally, miR-139-5p mimic causes further decrease, whereas miR-139-5p inhibitor can dramatically rescue the decline in gene expression caused by this mutation. These findings suggest that the familial ASDII may be a result of an ACTC1 3′UTR gain-of-function mutation caused by the introduction of a new miR-139-5p target site. Our results provide the first evidence of a pathogenic mutation in the ACTC1 3′UTR that may be associated with familial isolated ASDII.
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26
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Pulignani S, Vecoli C, Sabina S, Foffa I, Ait-Ali L, Andreassi MG. 3'UTR SNPs and Haplotypes in the GATA4 Gene Contribute to the Genetic Risk of Congenital Heart Disease. ACTA ACUST UNITED AC 2016; 69:760-5. [PMID: 27118528 DOI: 10.1016/j.rec.2016.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/22/2015] [Indexed: 01/19/2023]
Abstract
INTRODUCTION AND OBJECTIVES Single-nucleotide polymorphisms within a microRNA binding site can have different effects on gene expression, influencing the risk of disease. This study aimed to evaluate the association between single-nucleotide polymorphisms and haplotypes in the 3'UTR of the GATA4 gene and congenital heart disease risk. METHODS Bioinformatics algorithms were used to analyze single-nucleotide polymorphisms in putative microRNA-binding sites of GATA4 3'UTR and to calculate the difference in free energy of hybridization (ΔFE, kcal/mol) for each wild-type vs the variant allele. RESULTS The study population comprised 146 Caucasian patients (73 males; 6.68 ± 7.79 years) and a 265 healthy newborn participants (147 males). The sum of all |ΔFE| was considered to predict the biological importance of single-nucleotide polymorphisms binding more microRNAs. Next, the 4 polymorphisms (+1158C > T, +1256 A > T, +1355 G > A, +1521C > G) with the highest predicted |ΔFEtot| (9.91, 14.85, 11.03, 21.66kcal/mol, respectively) were genotyped in a case-control study (146 patients and 250 controls). Applying a correction for multiple testing only the +1158 T allele was found to be associated with a reduced risk showing significant difference between patients and controls. Haplotype analysis showed that the T-T-G-C haplotype (more uncommon in congenital heart diseases than in controls) was associated with a significantly decreased risk (P = .03), while the rare C-A-A-C haplotype, which was very uncommon in controls (0.3%) compared with the disease (2.4%), was associated with a 4-fold increased risk of disease (P = .04). CONCLUSIONS Common variants in 3'UTR of the GATA4 gene jointly interact, affecting the congenital heart disease susceptibility, probably by altering microRNA posttranscriptional regulation.
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Affiliation(s)
- Silvia Pulignani
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
| | - Cecilia Vecoli
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy.
| | - Saverio Sabina
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
| | - Ilenia Foffa
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
| | - Lamia Ait-Ali
- Consiglio Nazionale delle Ricerche, Institute of Clinical Physiology, Pisa, Italy
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27
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Manjegowda DS, Karunakar P, Ramachandra NB. Effect of Structural Changes in Proteins Derived from GATA4 Nonsynonymous Single Nucleotide Polymorphisms in Congenital Heart Disease. Indian J Pharm Sci 2016; 77:735-41. [PMID: 26997702 PMCID: PMC4778234 DOI: 10.4103/0250-474x.174988] [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] [Indexed: 01/02/2023] Open
Abstract
Congenital heart disease is the most common type of birth defect. The single nucleotide polymorphism in GATA4 is associated with various congenital heart disease phenotypes. In the present study, we analysed the nonsynonymous single nucleotide polymorphism of GATA4, which are involved in congenital heart disease by predicting the changes in protein structures. Total of 49 nonsynonymous single nucleotide polymorphisms of GATA4 was screened from congenital heart disease patients of Mysore and also globally reported nonsynonymous single nucleotide polymorphisms. To understand the role of nonsynonymous single nucleotide polymorphisms, we mutated the sequence and translated into amino acids. Further the mutated protein secondary structure is predicted and tertiary structure is predicted using homology modeling. The quantitative evaluation of protein structure quality was verified with Volume Area Dihedral Angle Reporter server. Results revealed the secondary, tertiary structural changes along with changes in free energy of folding, volume and accessible surface area. Thus, the structural changes in the mutated proteins impaired the normal function of GATA4.
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Affiliation(s)
- D S Manjegowda
- NUCSER, K S Hegde Medical Academy, NITTE University, Deralakatte, Mangalore-575 018, India
| | - P Karunakar
- Department of Biotechnology, PES Institute of Technology, BSK III Stage, Bengaluru-560 085, India, India
| | - N B Ramachandra
- Department of Studies in Zoology, Genomics Laboratory, University of Mysore, Manasagangotri, Mysore-570 006, India
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28
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Cao Y, Wang J, Wei C, Hou Z, Li Y, Zou H, Meng M, Wang W, Jiang L. Genetic variations of NKX2-5 in sporadic atrial septal defect and ventricular septal defect in Chinese Yunnan population. Gene 2016; 575:29-33. [DOI: 10.1016/j.gene.2015.08.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/21/2015] [Accepted: 08/16/2015] [Indexed: 01/06/2023]
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29
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Functional characterization of CDK5 and CDK5R1 mutations identified in patients with non-syndromic intellectual disability. J Hum Genet 2015; 61:283-93. [PMID: 26657932 DOI: 10.1038/jhg.2015.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/27/2015] [Accepted: 11/06/2015] [Indexed: 12/13/2022]
Abstract
Cyclin-dependent kinase 5 (CDK5) and cyclin-dependent kinase 5, regulatory subunit 1 (CDK5R1), encoding CDK5 activator p35, have a fundamental role in central nervous system (CNS) development and function, and are involved in the pathogenesis of several neurodegenerative disorders, thus constituting strong candidate genes for the onset of intellectual disability (ID). We carried out a mutation screening of CDK5 and CDK5R1 coding regions and CDK5R1 3'-UTR on a cohort of 360 patients with non-syndromic ID (NS-ID) using denaturing high performance liquid chromatography (DHPLC) and direct sequencing. We found one novel silent mutation in CDK5 and one novel silent mutation in CDK5R1 coding regions, three novel intronic variations in CDK5, not causing any splicing defect, and four novel heterozygous variations in CDK5R1 3'-UTR. None of these variations was present in 450 healthy controls and single-nucleotide polymorphism (SNP) databases. The functional study of CDK5R1 p.A108V mutation evidenced an impaired p35 cleavage by the calcium-dependent protease calpain. Moreover, luciferase constructs containing the CDK5R1 3'-UTR mutations showed altered gene expression levels. Eight known polymorphisms were also identified displaying different frequencies in NS-ID patients compared with the controls. In particular, the minor allele of CDK5R1 3'-UTR rs735555 polymorphism was associated with increased risk for NS-ID. In conclusion, our data suggest that mutations and polymorphisms in CDK5 and CDK5R1 genes may contribute to the onset of the NS-ID phenotype.
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30
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Cao Y, Lan W, Li Y, Wei C, Zou H, Jiang L. Single nucleotide polymorphism of NKX2-5 gene with sporadic congenital heart disease in Chinese Bai population. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:14917-24. [PMID: 26823822 PMCID: PMC4713608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common birth abnormality, especially for sporadic CHD. However, the etiology of sporadic CHD is largely unknown. NKX2-5, the earliest sign of cardiac progenitor cell differentiation, plays a key role in cardiac morphogenesis, and the mutation of this gene can cause sporadic CHD. PURPOSE To investigate the association of genetic variations of NKX2-5 with sporadic CHD in Chinese Bai people. METHODS The whole 2 coding exons and flanking intron sequences of NKX2-5 gene were screened using DNA sequencing in 70 Chinese Bai patients with sporadic CHD and 136 healthy controls. RESULTS A novel heterozygous DNA sequence variant (DSV), 1433A>G, was identified in one tetralogy of Fallot (TOF) patient and one persistent left superior vena cava (PLSVC) patient, but none in controls. The frequency of single nucleotide polymorphism (SNP) rs2277923 in CHD group was significantly higher than that in control group. The allele and genotype were associated with the occurrence of CHD. CONCLUSION The novel DSV (1433A>G) may be relevant with TOF and PLSVC, and the SNP rs2277923 of NKX2-5 gene contributes to the risk of sporadic CHD in Chinese Bai people.
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Affiliation(s)
- Yu Cao
- Yan'an Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming Yan'an Hospital Kunming 650051, China
| | - Weixing Lan
- Liuzhou Municipal Liutie Central Hospital Liuzhou 545007, China
| | - Yaxiong Li
- Yan'an Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming Yan'an Hospital Kunming 650051, China
| | - Chuanyu Wei
- Yan'an Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming Yan'an Hospital Kunming 650051, China
| | - Honglin Zou
- Yan'an Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming Yan'an Hospital Kunming 650051, China
| | - Lihong Jiang
- Yan'an Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming Yan'an Hospital Kunming 650051, China
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31
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Wilson KD, Shen P, Fung E, Karakikes I, Zhang A, InanlooRahatloo K, Odegaard J, Sallam K, Davis RW, Lui GK, Ashley EA, Scharfe C, Wu JC. A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases. Circ Res 2015; 117:603-11. [PMID: 26265630 DOI: 10.1161/circresaha.115.306723] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/27/2015] [Indexed: 12/21/2022]
Abstract
RATIONALE Thousands of mutations across >50 genes have been implicated in inherited cardiomyopathies. However, options for sequencing this rapidly evolving gene set are limited because many sequencing services and off-the-shelf kits suffer from slow turnaround, inefficient capture of genomic DNA, and high cost. Furthermore, customization of these assays to cover emerging targets that suit individual needs is often expensive and time consuming. OBJECTIVE We sought to develop a custom high throughput, clinical-grade next-generation sequencing assay for detecting cardiac disease gene mutations with improved accuracy, flexibility, turnaround, and cost. METHODS AND RESULTS We used double-stranded probes (complementary long padlock probes), an inexpensive and customizable capture technology, to efficiently capture and amplify the entire coding region and flanking intronic and regulatory sequences of 88 genes and 40 microRNAs associated with inherited cardiomyopathies, congenital heart disease, and cardiac development. Multiplexing 11 samples per sequencing run resulted in a mean base pair coverage of 420, of which 97% had >20× coverage and >99% were concordant with known heterozygous single nucleotide polymorphisms. The assay correctly detected germline variants in 24 individuals and revealed several polymorphic regions in miR-499. Total run time was 3 days at an approximate cost of $100 per sample. CONCLUSIONS Accurate, high-throughput detection of mutations across numerous cardiac genes is achievable with complementary long padlock probe technology. Moreover, this format allows facile insertion of additional probes as more cardiomyopathy and congenital heart disease genes are discovered, giving researchers a powerful new tool for DNA mutation detection and discovery.
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Affiliation(s)
- Kitchener D Wilson
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
| | - Peidong Shen
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Eula Fung
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Ioannis Karakikes
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Angela Zhang
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Kolsoum InanlooRahatloo
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Justin Odegaard
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Karim Sallam
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Ronald W Davis
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - George K Lui
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Euan A Ashley
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Curt Scharfe
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA
| | - Joseph C Wu
- From the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
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Muscle connective tissue controls development of the diaphragm and is a source of congenital diaphragmatic hernias. Nat Genet 2015; 47:496-504. [PMID: 25807280 PMCID: PMC4414795 DOI: 10.1038/ng.3250] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/23/2015] [Indexed: 12/14/2022]
Abstract
The diaphragm is an essential mammalian skeletal muscle, and defects in diaphragm development are the cause of congenital diaphragmatic hernias (CDH), a common and often lethal birth defect. The diaphragm is derived from multiple embryonic sources, but how these give rise to the diaphragm is unknown and, despite the identification of many CDH-associated genes, the etiology of CDH is incompletely understood. Using mouse genetics, we show that the pleuroperitoneal folds (PPFs), transient embryonic structures, are the source of the diaphragm’s muscle connective tissue, regulate muscle development, and their striking migration controls diaphragm morphogenesis. Furthermore, Gata4 mosaic mutations in PPF-derived muscle connective tissue fibroblasts result in the development of localized amuscular regions that are biomechanically weaker and more compliant and lead to CDH. Thus the PPFs and muscle connective tissue are critical for diaphragm development and mutations in PPF-derived fibroblasts are a source of CDH.
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Mattapally S, Nizamuddin S, Murthy KS, Thangaraj K, Banerjee SK. c.620C>T mutation in GATA4 is associated with congenital heart disease in South India. BMC MEDICAL GENETICS 2015; 16:7. [PMID: 25928801 PMCID: PMC4422155 DOI: 10.1186/s12881-015-0152-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/30/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND Congenital heart diseases (CHDs) usually refer to abnormalities in the structure and/or function of the heart that arise before birth. GATA4 plays an important role in embryonic heart development, hence the aim of this study was to find the association of GATA4 mutations with CHD among the south Indian CHD patients. METHOD GATA4 gene was sequenced in 100 CHD patients (ASD, VSD, TOF and SV) and 200 controls. Functional significance of the observed GATA4 mutations was analyzed using PolyPhen, SIFT, PMut, Plink, Haploview, ESE finder 3.0 and CONSITE. RESULTS We observed a total of 19 mutations, of which, one was in 5' UTR, 10 in intronic regions, 3 in coding regions and 5 in 3' UTR. Of the above mutations, one was associated with Atrial Septal Defect (ASD), two were found to be associated with Tetralogy of Fallot (TOF) and three (rs804280, rs4841587 and rs4841588) were strongly associated with Ventricular Septal Defect (VSD). Interestingly, one promoter mutation (-490 to 100 bp) i.e., 620 C>T (rs61277615, p-value = 0.008514), one splice junction mutation (G>A rs73203482; p-value = 9.6e-3, OR = 6.508) and one intronic mutation rs4841587 (p-value = 4.6e-3, OR = 4.758) were the most significant findings of this study. In silico analysis also proves that some of the mutations reported above are pathogenic. CONCLUSION The present study found that GATA4 genetic variations are associated with ASD, TOF and VSD in South Indian patients. In silico analysis provides further evidence that some of the observed mutations are pathogenic.
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Affiliation(s)
- Saidulu Mattapally
- Division of Pharmacology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India.
| | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
| | - Kona Samba Murthy
- Innova Children's Heart Hospital, Tarnaka, Hyderabad, 500017, India.
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
| | - Sanjay K Banerjee
- Division of Pharmacology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500 007, India. .,Current Address: Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), Gurgaon, HR-122016, Haryana, India.
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Vecoli C, Pulignani S, Foffa I, Andreassi MG. Congenital heart disease: the crossroads of genetics, epigenetics and environment. Curr Genomics 2014; 15:390-9. [PMID: 25435801 PMCID: PMC4245698 DOI: 10.2174/1389202915666140716175634] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/24/2014] [Accepted: 07/07/2014] [Indexed: 02/07/2023] Open
Abstract
Congenital heart diseases (CHDs) are recognized as the most common type of birth malformations. Although recent advances in pre- and neonatal diagnosis as well as in surgical procedures have reduced the morbidity and mortality for many CHD, the etiology for CHD remains undefined. In non-syndromic and isolated (without a familial history or a Mendelian inheritance) forms of CHDs, a multifactorial pathogenesis with interplay between inherited and non-inherited causes is recognized. In this paper, we discuss the current knowledge of the potential molecular mechanisms, mediating abnormal cardiac development in non-syndromic and isolated CHD, including mutations in cardiac transcription factors, the role of somatic mutations and epigenetic alterations as well as the influence of gene-environment interactions. In the near future, the advent of high-throughput genomic technologies with the integration of system biology will expand our understanding of isolated, non-syndromic CHDs for their prevention, early diagnosis and therapy.
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Affiliation(s)
| | | | - Ilenia Foffa
- CNR, Institute of Clinical Physiology, Massa, Italy
| | - Maria Grazia Andreassi
- CNR, Institute of Clinical Physiology, Pisa, Italy ; Fondazione Toscana G.Monasterio, Massa, Italy
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Melanocortin-4 receptor (MC4R) polymorphisms are associated with growth and meat quality traits in sheep. Mol Biol Rep 2014; 41:6967-74. [DOI: 10.1007/s11033-014-3583-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 07/05/2014] [Indexed: 12/21/2022]
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Wnt signaling pathway pharmacogenetics in non-small cell lung cancer. THE PHARMACOGENOMICS JOURNAL 2014; 14:509-22. [PMID: 24980784 PMCID: PMC4237616 DOI: 10.1038/tpj.2014.21] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 04/02/2014] [Accepted: 04/15/2014] [Indexed: 12/27/2022]
Abstract
Wnt/β-catenin pathway alterations in non-small cell lung cancer (NSCLC) are associated with poor prognosis and resistance. In 598 stage III-IV NSCLC patients receiving platinum-based chemotherapy at MD Anderson Cancer Center (MDACC), we correlated survival with 441 host SNPs in 50 Wnt pathway genes. We then assessed the most significant SNPs in 240 Mayo Clinic patients receiving platinum-based chemotherapy for advanced NSCLC, 127 MDACC patients receiving platinum-based adjuvant chemotherapy and 340 early stage MDACC patients undergoing surgery alone (cohorts 2–4). In multivariate analysis, survival correlates with SNPs for AXIN2 (rs11868547 and rs4541111, of which rs11868547 was assessed in cohorts 2–4), Wnt-5B (rs12819505), CXXC4 (rs4413407) and WIF-1 (rs10878232). Median survival was 19.7, 15.6, and 10.7 months for patients with 1, 2, and 3–5 unfavorable genotypes, respectively (p= 3.8×10−9). Survival tree analysis classified patients into two groups (MST 11.3 vs 17.3 months, p=4.7×10−8). None of the SNPs achieved significance in cohorts 2–4; however, there was a trend in the same direction as cohort 1 for 3 of the SNPs. Using online databases, we found rs10878232 displayed expression quantitative trait loci (eQTL) correlation with the expression of LEMD3, a neighboring gene previously associated with NSCLC survival. In conclusion, results from cohort 1 provide further evidence for an important role for Wnt in NSCLC. Investigation of Wnt inhibitors in advanced NSCLC would be reasonable. Lack of a SNP association with outcome in cohorts 2–4 could be due to low statistical power, impact of patient heterogeneity, or false positive observations in cohort 1.
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Stachowiak M, Szydlowski M, Flisikowski K, Flisikowska T, Bartz M, Schnieke A, Switonski M. Polymorphism in 3' untranslated region of the pig PPARA gene influences its transcript level and is associated with adipose tissue accumulation. J Anim Sci 2014; 92:2363-71. [PMID: 24671595 DOI: 10.2527/jas.2013-7509] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The PPARA (peroxisome proliferator-activated receptor-α) gene encodes a nuclear receptor that plays an important role in fatty acid catabolism by transcriptional regulation of genes involved in fatty acid oxidation and can be considered as a candidate gene for fatness traits in the pig. The aim of the study was to search for a functional polymorphism in 3' untranslated region (UTR), their association with production traits, and postnatal PPARA transcript level in 2 skeletal muscles (longissimus and semimembranosus) of 5 commercial pig breeds (Polish Landrace [PL], Polish Large White [PLW], Duroc, Pietrain, and Pulawska). Altogether, 9 novel polymorphisms (8 SNP and 1 indel) were found in the 3' UTR. The in silico analysis revealed 6 putative microRNA target sequences in the analyzed region. The c.*636A>G substitution was widely distributed across breeds and located near the putative target sequence for miR-224. The relative PPARA transcript level was higher (P < 0.05) in LM of AA than in those of GG homozygous animals for SNP c.*636A>G. The luciferase assay revealed that miR-224 probably acts as a negative regulator of the PPARA expression in pig adipocytes (P = 2.9 × 10(-7)), but we did not observe the effect of the A or G alleles on the interaction between miR-224 and its putative target sequence. We hypothesize that the 2 predominant haplotypes, differing at 4 sites (including c.*636A>G), present different architecture of its 3' UTR and it could affect the level of the transcript. The c.*636A>G SNP, analyzed in PL and PLW, was significantly associated with backfat thickness at 3 points (P < 0.05) and intramuscular fat content (P < 0.01) in PL. Suggestive associations were found between 4 SNP (c.*321A>C, c.*324G>C, c.*626T>C, and c.*636A>G) and fatty acid contents in LM and subcutaneous and visceral fat tissue of PL, PLW, Duroc and Pietrain pigs. The PPARA mRNA level was higher in semimembranosus muscle than in LM (P = 8.38 × 10(-12)) in a general comparison and the same trend was found in most breeds (except for PL) and at all tested days of age (60, 90, 120, 150, 180, and 210 d). The effect of breed was highly significant in a general comparison (P = 0.48 × 10(-8)), but there was no common expression pattern in both muscles among different age groups. We conclude that the c.*636A>G SNP in the PPARA gene can be considered in PL breed as a useful genetic marker for adipose tissue accumulation.
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Affiliation(s)
- M Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - M Szydlowski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - K Flisikowski
- Chair of Livestock Biotechnology, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - T Flisikowska
- Chair of Livestock Biotechnology, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - M Bartz
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - A Schnieke
- Chair of Livestock Biotechnology, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - M Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
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Huang RT, Xue S, Xu YJ, Zhou M, Yang YQ. Somatic GATA5 mutations in sporadic tetralogy of Fallot. Int J Mol Med 2014; 33:1227-35. [PMID: 24573614 DOI: 10.3892/ijmm.2014.1674] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/11/2014] [Indexed: 11/06/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease, with high morbidity and mortality rates. Accumulating evidence has demonstrated that genetic defects play an important role in the pathogenesis of TOF. However, the molecular basis of TOF in the majority of patients remains to be determined. In the present study, sequence analysis of the coding exons and exon-intron boundaries of GATA5, a gene encoding a zinc finger‑containing transcriptional factor crucial for cardiogenesis, was performed on genomic DNA isolated from resected cardiac tissue and matched blood samples of 85 unrelated patients who underwent surgical repair of TOF. Genotyping was performed on the cardiac tissue and matched blood samples from 63 unrelated patients who underwent cardiac valve replacement due to rheumatic heart disease as well as the blood samples obtained from 200 unrelated healthy individuals. The functional effect of the mutations was evaluated by using a luciferase reporter assay system. As a result, the novel heterozygous GATA5 mutations, p.D203E and p.Y208X, were found in the cardiac tissues of two TOF patients, respectively. There were no mutations in the cardiac tissues obtained from 63 patients with rheumatic heart disease nor in the blood samples obtained from the 348 subjects. Functional analysis revealed that the GATA5 mutants were consistently associated with significantly decreased transcriptional activity compared with their wild-type counterpart. Thus, results of this study showed an association of somatic GATA5 mutations with TOF, providing further insight into the underlying molecular mechanism of TOF.
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Affiliation(s)
- Ri-Tai Huang
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Song Xue
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Ying-Jia Xu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Min Zhou
- Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
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Muiya NP, Wakil SM, Tahir AI, Hagos S, Najai M, Gueco D, Al-Tassan N, Andres E, Mazher N, Meyer BF, Dzimiri N. A study of the role of GATA4 polymorphism in cardiovascular metabolic disorders. Hum Genomics 2013; 7:25. [PMID: 24330461 PMCID: PMC3899629 DOI: 10.1186/1479-7364-7-25] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/01/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The study was designed to evaluate the association of GATA4 gene polymorphism with coronary artery disease (CAD) and its metabolic risk factors, including dyslipidaemic disorders, obesity, type 2 diabetes and hypertension, following a preliminary study linking early onset of CAD in heterozygous familial hypercholesterolaemia to chromosome 8, which harbours the GATA4 gene. RESULTS We first sequenced the whole GATA4 gene in 250 individuals to identify variants of interest and then investigated the association of 12 single-nucleotide polymorphisms (SNPs) with the disease traits using Taqman chemistry in 4,278 angiographed Saudi individuals. Of the studied SNPs, rs804280 (1.14 (1.03 to 1.27); p = 0.009) was associated with CAD (2,274 cases vs 2,004 controls), hypercholesterolaemia (1,590 vs 2,487) (1.61 (1.03-2.52); p = 0.037) and elevated low-density lipoprotein-cholesterol (hLDLC) (575 vs 3,404) (1.87 (1.10-3.15); p = 0.020). Additionally, rs3729855_T (1.52 (1.09-2.11; p = 0.013)) and rs17153743 (AG + GG) (2.30 (1.30-4.26); p = 0.005) were implicated in hypertension (3,312 vs 966), following adjustments for confounders. Furthermore, haplotypes CCCGTGCC (χ2 = 4.71; p = 0.041) and GACCCGTG (χ2 = 3.84; p = 0.050) constructed from the SNPs were associated with CAD and ACCCACGC (χ2 = 6.58; p = 0.010) with myocardial infarction, while hypercholesterolaemia (χ2 = 3.86; p = 0.050) and hLDLC (χ2 = 4.94; p = 0.026) shared the AACCCATGT, and AACCCATGTC was associated with hLDLC (χ2 = 4.83; p = 0.028). A 10-mer GACCCGCGCC (χ2 = 7.59; p = 0.006) was associated with obesity (1,631 vs 2,362), and the GACACACCC (χ2 = 4.05; p = 0.044) was implicated in type 2 diabetes mellitus 2,378 vs 1,900). CONCLUSION Our study implicates GATA4 in CAD and its metabolic risk traits. The finding also points to the possible involvement of yet undefined entities related to GATA4 transcription activity or gene regulatory pathways in events leading to these cardiovascular disorders.
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Affiliation(s)
- Nzioka P Muiya
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Salma M Wakil
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Asma I Tahir
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Samya Hagos
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Najai
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Daisy Gueco
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nada Al-Tassan
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Editha Andres
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nejat Mazher
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Brian F Meyer
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nduna Dzimiri
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
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Dirkx E, da Costa Martins PA, De Windt LJ. Regulation of fetal gene expression in heart failure. Biochim Biophys Acta Mol Basis Dis 2013; 1832:2414-24. [PMID: 24036209 DOI: 10.1016/j.bbadis.2013.07.023] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/15/2013] [Accepted: 07/23/2013] [Indexed: 01/24/2023]
Abstract
During the processes leading to adverse cardiac remodeling and heart failure, cardiomyocytes react to neurohumoral stimuli and biomechanical stress by activating pathways that induce pathological hypertrophy. The gene expression patterns and molecular changes observed during cardiac hypertrophic remodeling bare resemblance to those observed during fetal cardiac development. The re-activation of fetal genes in the adult failing heart is a complex biological process that involves transcriptional, posttranscriptional and epigenetic regulation of the cardiac genome. In this review, the mechanistic actions of transcription factors, microRNAs and chromatin remodeling processes in regulating fetal gene expression in heart failure are discussed.
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Affiliation(s)
- Ellen Dirkx
- Dept of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, The Netherlands; ICIN-Netherlands Heart Institute, Royal Netherlands Academy of Sciences, Utrecht, The Netherlands
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Michalova E, Vojtesek B, Hrstka R. Impaired pre-mRNA processing and altered architecture of 3' untranslated regions contribute to the development of human disorders. Int J Mol Sci 2013; 14:15681-94. [PMID: 23896598 PMCID: PMC3759880 DOI: 10.3390/ijms140815681] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 11/16/2022] Open
Abstract
The biological fate of each mRNA and consequently, the protein to be synthesised, is highly dependent on the nature of the 3' untranslated region. Despite its non-coding character, the 3' UTR may affect the final mRNA stability, the localisation, the export from the nucleus and the translation efficiency. The conserved regulatory sequences within 3' UTRs and the specific elements binding to them enable gene expression control at the posttranscriptional level and all these processes reflect the actual state of the cell including proliferation, differentiation, cellular stress or tumourigenesis. Through this article, we briefly outline how the alterations in the establishment and final architecture of 3' UTRs may contribute to the development of various disorders in humans.
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Affiliation(s)
- Eva Michalova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno 656 53, Czech Republic; E-Mails: (E.M.); (B.V.)
| | - Borivoj Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno 656 53, Czech Republic; E-Mails: (E.M.); (B.V.)
| | - Roman Hrstka
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno 656 53, Czech Republic; E-Mails: (E.M.); (B.V.)
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Wang E, Sun S, Qiao B, Duan W, Huang G, An Y, Xu S, Zheng Y, Su Z, Gu X, Jin L, Wang H. Identification of functional mutations in GATA4 in patients with congenital heart disease. PLoS One 2013; 8:e62138. [PMID: 23626780 PMCID: PMC3633926 DOI: 10.1371/journal.pone.0062138] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 03/19/2013] [Indexed: 01/10/2023] Open
Abstract
Congenital heart disease (CHD) is one of the most prevalent developmental anomalies and the leading cause of noninfectious morbidity and mortality in newborns. Despite its prevalence and clinical significance, the etiology of CHD remains largely unknown. GATA4 is a highly conserved transcription factor that regulates a variety of physiological processes and has been extensively studied, particularly on its role in heart development. With the combination of TBX5 and MEF2C, GATA4 can reprogram postnatal fibroblasts into functional cardiomyocytes directly. In the past decade, a variety of GATA4 mutations were identified and these findings originally came from familial CHD pedigree studies. Given that familial and sporadic CHD cases allegedly share a basic genetic basis, we explore the GATA4 mutations in different types of CHD. In this study, via direct sequencing of the GATA4 coding region and exon-intron boundaries in 384 sporadic Chinese CHD patients, we identified 12 heterozygous non-synonymous mutations, among which 8 mutations were only found in CHD patients when compared with 957 controls. Six of these non-synonymous mutations have not been previously reported. Subsequent functional analyses revealed that the transcriptional activity, subcellular localization and DNA binding affinity of some mutant GATA4 proteins were significantly altered. Our results expand the spectrum of GATA4 mutations linked to cardiac defects. Together with the newly reported mutations, approximately 110 non-synonymous mutations have currently been identified in GATA4. Our future analysis will explore why the evolutionarily conserved GATA4 appears to be hypermutable.
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Affiliation(s)
- Erli Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuna Sun
- Children’s Hospital of Fudan University, Shanghai, China
| | - Bin Qiao
- Institute of Cardiovascular Disease General Hospital of Jinan Military Region, Jinan, China
| | - Wenyuan Duan
- Institute of Cardiovascular Disease General Hospital of Jinan Military Region, Jinan, China
| | - Guoying Huang
- Children’s Hospital of Fudan University, Shanghai, China
| | - Yu An
- Children’s Hospital of Fudan University, Shanghai, China
- The Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shuhua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yufang Zheng
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhixi Su
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xun Gu
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongyan Wang
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- The Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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43
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Sabina S, Pulignani S, Rizzo M, Cresci M, Vecoli C, Foffa I, Ait-Ali L, Pitto L, Andreassi MG. Germline hereditary, somatic mutations and microRNAs targeting-SNPs in congenital heart defects. J Mol Cell Cardiol 2013; 60:84-9. [PMID: 23583740 DOI: 10.1016/j.yjmcc.2013.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/22/2013] [Accepted: 04/04/2013] [Indexed: 12/21/2022]
Abstract
Somatic mutations and dysregulation by microRNAs (miRNAs) may have a pivotal role in the Congenital Heart Defects (CHDs). The purpose of the study was to assess both somatic and germline mutations in the GATA4 and NKX2.5 genes as well as to identify 3'UTR single nucleotide polymorphisms (SNPs) in the miRNA target sites. We enrolled 30 patients (13 males; 13.4±8.3 years) with non-syndromic CHD. GATA4 and NKX2.5 genes were screened in cardiac tissue of sporadic and in blood samples of familial cases. Computational methods were used to detect putative miRNAs in the 3'UTR region and to assess the Minimum Free Energy of hybridization (MFE, kcal/mol). Difference of MFEs (ΔMFE) ≥4 kcal/mol between alleles was considered biologically relevant on miRNA binding. The sum of all ΔMFEs (|ΔMFEtot|=∑|ΔMFE|) was calculated in order to predict the biological importance of SNPs binding more miRNAs. No evidence of novel GATA4 and NKX2.5 mutations was found both in sporadic and familial patients. Bioinformatic analysis revealed 27 putative miRNAs binding to identified SNPs in the 3'UTR of GATA4. ΔMFE ≥4 kcal/mol between alleles was obtained for the +354A>C (miR-4299), +587A>G (miR-604), +1355G>A (miR-548v, miR-139-5p) and +1521C>G (miR-583, miR-3125, miR-3928) SNPs. The +1521C>G SNP showed the highest ΔMFEtot (21.66 kcal/mol). Luciferase reporter assays indicated that miR-583 was dose-dependently effective in regulating +1521 C allele compared with +1521 G allele. Based on the analysis of 100 CHD cases and 204 healthy newborns, the +1521 G allele was also associated with a lower risk of CHD (OR=0.5, 95% CI 0.3-0.9, p=0.03), likely due to the relatively low binding of the miRNA and high levels of protein. These results suggest that common SNPs in the 3'UTR of GATA4 alter miRNA gene regulation contributing to the pathogenesis of CHDs.
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Cheng C, Lin Y, Yang F, Wang W, Wu C, Qin J, Shao X, Zhou L. Mutational screening of affected cardiac tissues and peripheral blood cells identified novel somatic mutations in GATA4 in patients with ventricular septal defect. J Biomed Res 2013; 25:425-30. [PMID: 23554720 PMCID: PMC3596722 DOI: 10.1016/s1674-8301(11)60056-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 07/31/2011] [Accepted: 10/05/2011] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to examine how somatic mutations of the GATA4 gene contributed to the genesis of ventricular septal defect (VSD). The coding and intron-exon boundary regions of GATA4 were sequenced of DNA samples from peripheral blood cells and cardiac tissues of twenty surgically treated probands with VSD. Seven novel heterozygous variants were detected in cardiac tissues from VSD patients, but they were not detected in the peripheral blood cells of VSD patients or in 500 healthy control samples. We replicated 14 single nucleotide polymorphisms (SNPs) reported in NCBI. Bioinformatics analysis was performed to analyze the possible mechanism by which mutations were linked to VSD. Among those variants, c. 1004C>A (p.S335X) occurred in the highly conserved domain of GATA4 and generated a termination codon, which led to the production of truncated GATA4. The seven novel heterozygous GATA4 mutations were only identified in cardiac tissues with VSD, suggesting that they are of somatic origin. A higher mutation rate in cardiac tissues than in peripheral blood cells implies that the genetic contribution to VSD may have been underestimated.
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Affiliation(s)
- Chunyan Cheng
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Huang RT, Xue S, Xu YJ, Yang YQ. Somatic mutations in the GATA6 gene underlie sporadic tetralogy of Fallot. Int J Mol Med 2012; 31:51-8. [PMID: 23175051 DOI: 10.3892/ijmm.2012.1188] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 10/22/2012] [Indexed: 11/05/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease associated with significant morbidity and mortality in humans. However, the molecular etiology underlying TOF in most patients remains largely unknown. In the present study, sequence analysis of the GATA6 gene was performed from fresh-frozen cardiac tissues and matched blood samples of 52 unrelated patients who underwent surgical repair of TOF. The cardiac tissues and matched blood specimens from 46 patients who underwent cardiac valve replacement due to rheumatic heart disease and blood samples from 200 healthy individuals as controls were genotyped. The functional characteristics of the mutations were assessed using a luciferase reporter assay system. Based on the results, two novel heterozygous GATA6 mutations, p.G367X and p.G394C, were identified in the cardiac tissues of 2 TOF patients, respectively. No mutations were found in the cardiac tissues from 46 patients with rheumatic heart disease and in the blood samples from the 298 participants. Functional analysis demonstrated that the GATA6 mutants were consistently associated with significantly reduced transcriptional activation compared with their wild-type counterpart. This is the first report on the link of somatic GATA6 mutation to TOF, providing novel insight into the molecular mechanism involved in TOF.
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Affiliation(s)
- Ri-Tai Huang
- Department of Cardiothoracic Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200127, PR China
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46
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Sowa N, Horie T, Kuwabara Y, Baba O, Watanabe S, Nishi H, Kinoshita M, Takanabe‐Mori R, Wada H, Shimatsu A, Hasegawa K, Kimura T, Ono K. MicroRNA 26b encoded by the intron of small CTD phosphatase (SCP) 1 has an antagonistic effect on its host gene. J Cell Biochem 2012; 113:3455-65. [DOI: 10.1002/jcb.24222] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Naoya Sowa
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Takahiro Horie
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Yasuhide Kuwabara
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Osamu Baba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Shin Watanabe
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Hitoo Nishi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Minako Kinoshita
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Rieko Takanabe‐Mori
- Division of Translational Research, Kyoto Medical Center, National Hospital Organization, Kyoto 612‐8555, Japan
| | - Hiromichi Wada
- Division of Translational Research, Kyoto Medical Center, National Hospital Organization, Kyoto 612‐8555, Japan
| | - Akira Shimatsu
- Division of Translational Research, Kyoto Medical Center, National Hospital Organization, Kyoto 612‐8555, Japan
| | - Koji Hasegawa
- Division of Translational Research, Kyoto Medical Center, National Hospital Organization, Kyoto 612‐8555, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
| | - Koh Ono
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606‐8507, Japan
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47
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Liang M, Hole D, Wu J, Blake T, Wu Y. Expression and functional analysis of NUCLEAR FACTOR-Y, subunit B genes in barley. PLANTA 2012; 235:779-91. [PMID: 22042327 DOI: 10.1007/s00425-011-1539-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Accepted: 10/12/2011] [Indexed: 05/10/2023]
Abstract
NUCLEAR FACTOR-Y, subunit B (NF-YB) comprises a multigene family in plants and has been shown to play important roles in growth, development, and response to environmental stress. In this study, five NF-YBs containing the full-length coding region were obtained from barley (Hordeum vulgare) through database sequence analysis, cloning, and sequencing. Sequence alignment and phylogenetic analysis showed that HvNF-YB3 and HvNF-YB1 were clustered with NF-YB2 and NF-YB3 in Arabidopsis, suggesting these NF-YBs are evolutionary and functionally related. To test this hypothesis, HvNF-YB3 and HvNF-YB1 were overexpressed in Arabidopsis. Overexpression of HvNF-YB1 greatly promoted early flowering in Arabidopsis, supporting that HvNF-YB1may have conserved gene function in flowering time control as NF-YB2 and NF-YB3 in Arabidopsis. Overexpression of HvNF-YB3 in Arabidopsis had no effect on flowering time. An analysis of barley single-nucleotide polymorphism (SNP) data, however, revealed a significant association between an HvNF-YB3 SNP and heading date. While it is unknown whether HvNF-YB3 directly contributes to heading date regulation, the results implied that HvNF-YB3 may also have conserved function in flowering time (heading date in barley) control. Further studies are needed to directly verify these gene functions in barley. Barley NF-YBs showed different expression patterns associated with tissue types, developmental stages, and response to different stress treatments, suggesting that barley NF-YBs may be involved in other physiological processes.
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Affiliation(s)
- Mingxiang Liang
- Department of Plants, Soils, and Climate, Utah State University, Logan, UT 84322, USA.
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Breckpot J, Thienpont B, Gewillig M, Allegaert K, Vermeesch JR, Devriendt K. Differences in Copy Number Variation between Discordant Monozygotic Twins as a Model for Exploring Chromosomal Mosaicism in Congenital Heart Defects. Mol Syndromol 2012; 2:81-87. [PMID: 22511896 DOI: 10.1159/000335284] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2011] [Indexed: 12/21/2022] Open
Abstract
Studies addressing the role of somatic copy number variation (CNV) in the genesis of congenital heart defects (CHDs) are scarce, as cardiac tissue is difficult to obtain, especially in non-affected individuals. We explored the occurrence of copy number differences in monozygotic (MZ) twins discordant for the presence of a CHD, as an illustrative model for chromosomal mosaicism in CHDs. Array comparative genomic hybridization was performed on peripheral blood-derived DNA obtained from 6 discordant MZ twin pairs and on sex-matched reference samples. To identify CNV differences between both twin members as well as potential CNVs in both twins contributing to the phenotype, DNA from each twin was hybridized against its co-twin, and against a normal control. Three copy number differences in 1 out of 6 MZ twin pairs were detected, confirming the occurrence of somatic CNV events in MZ twins. Further investigation by copy number and (epi)genome sequencing analyses in MZ twins, discordant for the presence of CHDs, is required to improve our knowledge on how postzygotic genetic, environmental and stochastic factors can affect human heart development.
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Affiliation(s)
- J Breckpot
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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Han M, Yang Z, Sayed D, He M, Gao S, Lin L, Yoon S, Abdellatif M. GATA4 expression is primarily regulated via a miR-26b-dependent post-transcriptional mechanism during cardiac hypertrophy. Cardiovasc Res 2012; 93:645-54. [PMID: 22219180 DOI: 10.1093/cvr/cvs001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIMS GATA4 is a transcription factor that is up-regulated during cardiac hypertrophy and plays a fundamental role in myocyte growth and survival. In this study, we investigate the transcriptional vs. post-transcriptional mechanisms that are involved in regulating GATA4 in the heart during neonatal and pressure overload-induced hypertrophic growth. METHODS AND RESULTS GATA4 protein is significantly higher during pressure overload-induced (2.9 ± 0.4-fold) and neonatal (6.8 ± 1-fold) hypertrophic growth vs. the normal adult mouse heart. Using RNA polymerase II immunoprecipitation combined with deep sequencing, we confirmed that active transcription of the Gata4 gene remained unchanged during hypertrophy, whereas it was two-fold higher in the neonatal vs. adult heart, commensurate with the mRNA levels. These results suggested a post-transcriptional mode of regulation of its expression, which prompted the identification of a conserved sequence in its 3'-untranslated region that was responsible for reduced translation via miR-26b. Overexpression of miR-26b reduced GATA4-dependent transcription, endothelin-induced hypertrophy, and sensitized the cells to apoptotic insults. Additionally, miR-26b targeted phospholipase C-β1, which, in turn, inhibited miR-26b expression, creating a double-negative feedback loop. Accordingly, overexpression of miR-26b in the heart inhibited up-regulation of its targets and the development of hypertrophy. However, knockdown of miR-26b is not sufficient for inducing hypertrophy. CONCLUSION Down-regulation of miR-26b in the heart is required for the up-regulation of GATA4 and the induction of pressure-induced cardiac hypertrophy. The results also underscore the functional relevance of miRNAs in regulating gene expression during cardiac hypertrophy.
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Affiliation(s)
- Mingyue Han
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
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Abstract
Congenital heart disease is a major cause of morbidity and mortality throughout life. Mutations in numerous transcription factors have been identified in patients and families with some of the most common forms of cardiac malformations and arrhythmias. This review discusses transcription factor pathways known to be important for normal heart development and how abnormalities in these pathways have been linked to morphological and functional forms of congenital heart defects. A comprehensive, current list of known transcription factor mutations associated with congenital heart disease is provided, but the review focuses primarily on three key transcription factors, Nkx2-5, GATA4, and Tbx5, and their known biochemical and genetic partners. By understanding the interaction partners, transcriptional targets, and upstream activators of these core cardiac transcription factors, additional information about normal heart formation and further insight into genes and pathways affected in congenital heart disease should result.
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Affiliation(s)
- David J McCulley
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
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